{-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE QuasiQuotes #-} import Prelude hiding (lines, unlines) import Data.Text (Text, lines, unlines) import NeatInterpolation (text) import Test.Hspec import Test.QuickCheck import Data.Attoparsec.Text (parseOnly, endOfLine, parseTest, many') import Bio.Uniprot.Type import Bio.Uniprot.Parser idStr :: Text idStr = "ID PDCD1_HUMAN Reviewed; 288 AA." acStr :: Text acStr = "AC Q15116; O00517; Q8IX89;" dtStr :: Text dtStr = [text| DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot. DT 17-APR-2007, sequence version 3. DT 28-FEB-2018, entry version 163.|] deStr :: Text deStr = [text| DE RecName: Full=Programmed cell death protein 1; DE Short=Protein PD-1; DE Short=hPD-1; DE AltName: CD_antigen=CD279; DE Flags: Precursor;|] de2Str :: Text de2Str = [text| DE RecName: Full=Arginine biosynthesis bifunctional protein argJ; DE Includes: DE RecName: Full=Glutamate N-acetyltransferase; DE EC=2.3.1.35; DE AltName: Full=Ornithine acetyltransferase; DE Short=OATase; DE AltName: Full=Ornithine transacetylase; DE Includes: DE RecName: Full=Amino-acid acetyltransferase; DE EC=2.3.1.1; DE AltName: Full=N-acetylglutamate synthase; DE Short=AGS; DE Contains: DE RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain; DE Contains: DE RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain;|] gnStr :: Text gnStr = "GN Name=PDCD1; Synonyms=PD1;" osStr :: Text osStr = "OS Homo sapiens (Human)." ogStr :: Text ogStr = [text| OG Plasmid R6-5, Plasmid IncFII R100 (NR1), and OG Plasmid IncFII R1-19 (R1 drd-19).|] ocStr :: Text ocStr = [text| OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; OC Catarrhini; Hominidae; Homo.|] oxStr :: Text oxStr = "OX NCBI_TaxID=9606;" ohStr :: Text ohStr = "OH NCBI_TaxID=9536; Cercopithecus hamlyni (Owl-faced monkey) (Hamlyn's monkey)." refStr :: Text refStr = [text| RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=7851902; DOI=10.1006/geno.1994.1562; RA Shinohara T., Taniwaki M., Ishida Y., Kawaich M., Honjo T.; RT "Structure and chromosomal localization of the human PD-1 gene RT (PDCD1)."; RL Genomics 23:704-706(1994). RN [2] RP NUCLEOTIDE SEQUENCE [MRNA]. RX PubMed=9332365; DOI=10.1016/S0378-1119(97)00260-6; RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R., RA Burrows P.D., Billips L.D.; RT "The human PD-1 gene: complete cDNA, genomic organization, and RT developmentally regulated expression in B cell progenitors."; RL Gene 197:177-187(1997). RN [3] RP ERRATUM. RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R., RA Burrows P.D., Billips L.D.; RL Gene 203:253-253(1997). RN [4] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INVOLVEMENT IN SLEB2. RX PubMed=12402038; DOI=10.1038/ng1020; RA Prokunina L., Castillejo-Lopez C., Oberg F., Gunnarsson I., Berg L., RA Magnusson V., Brookes A.J., Tentler D., Kristjansdottir H., RA Grondal G., Bolstad A.I., Svenungsson E., Lundberg I., Sturfelt G., RA Jonssen A., Truedsson L., Lima G., Alcocer-Varela J., Jonsson R., RA Gyllensten U.B., Harley J.B., Alarcon-Segovia D., Steinsson K., RA Alarcon-Riquelme M.E.; RT "A regulatory polymorphism in PDCD1 is associated with susceptibility RT to systemic lupus erythematosus in humans."; RL Nat. Genet. 32:666-669(2002). RN [5] RP NUCLEOTIDE SEQUENCE [MRNA]. RA He X., Xu L., Liu Y., Zeng Y.; RT "Cloning of PD-1 cDNA from activated peripheral leukocytes."; RL Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases. RN [6] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Livingston R.J., Shaffer T., McFarland I., Nguyen C.P., Stanaway I.B., RA Rajkumar N., Johnson E.J., da Ponte S.H., Willa H., Ahearn M.O., RA Bertucci C., Acklestad J., Carroll A., Swanson J., Gildersleeve H.I., RA Nickerson D.A.; RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases. RN [7] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RX PubMed=14702039; DOI=10.1038/ng1285; RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S., RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.; RT "Complete sequencing and characterization of 21,243 full-length human RT cDNAs."; RL Nat. Genet. 36:40-45(2004). RN [8] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RX PubMed=15489334; DOI=10.1101/gr.2596504; RG The MGC Project Team; RT "The status, quality, and expansion of the NIH full-length cDNA RT project: the Mammalian Gene Collection (MGC)."; RL Genome Res. 14:2121-2127(2004). RN [9] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RA Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R., RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., RA Venter J.C.; RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases. RN [10] RP FUNCTION. RX PubMed=21276005; DOI=10.1111/j.1749-6632.2010.05919.x; RA Fife B.T., Pauken K.E.; RT "The role of the PD-1 pathway in autoimmunity and peripheral RT tolerance."; RL Ann. N. Y. Acad. Sci. 1217:45-59(2011).|] ccStr :: Text ccStr = [text| CC -!- FUNCTION: Inhibitory cell surface receptor involved in the CC regulation of T-cell function during immunity and tolerance. Upon CC ligand binding, inhibits T-cell effector functions in an antigen- CC specific manner. Possible cell death inducer, in association with CC other factors. {ECO:0000269|PubMed:21276005}. CC -!- SUBUNIT: Monomer. {ECO:0000250}. CC -!- INTERACTION: CC Q9NZQ7:CD274; NbExp=2; IntAct=EBI-4314328, EBI-4314282; CC Q9NZQ7-1:CD274; NbExp=2; IntAct=EBI-4314328, EBI-15686469; CC Q06124:PTPN11; NbExp=3; IntAct=EBI-4314328, EBI-297779; CC -!- SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane CC protein. CC -!- DEVELOPMENTAL STAGE: Induced at programmed cell death. CC -!- DISEASE: Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A CC chronic, relapsing, inflammatory, and often febrile multisystemic CC disorder of connective tissue, characterized principally by CC involvement of the skin, joints, kidneys and serosal membranes. It CC is of unknown etiology, but is thought to represent a failure of CC the regulatory mechanisms of the autoimmune system. The disease is CC marked by a wide range of system dysfunctions, an elevated CC erythrocyte sedimentation rate, and the formation of LE cells in CC the blood or bone marrow. {ECO:0000269|PubMed:12402038}. CC Note=Disease susceptibility is associated with variations CC affecting the gene represented in this entry.|] peStr :: Text peStr = "PE 1: Evidence at protein level;" kwStr :: Text kwStr = [text| KW 3D-structure; Apoptosis; Complete proteome; Disulfide bond; KW Glycoprotein; Immunity; Immunoglobulin domain; Membrane; Polymorphism; KW Reference proteome; Signal; Systemic lupus erythematosus; KW Transmembrane; Transmembrane helix.|] drStr :: Text drStr = [text| DR EMBL; L27440; AAC41700.1; -; Genomic_DNA. DR EMBL; U64863; AAC51773.1; -; mRNA. DR EMBL; AF363458; AAN64003.1; -; Genomic_DNA. DR EMBL; AY238517; AAO63583.1; -; mRNA. DR EMBL; EF064716; ABK41899.1; -; Genomic_DNA. DR EMBL; AK313848; BAG36577.1; -; mRNA. DR EMBL; CH471063; EAW71298.1; -; Genomic_DNA. DR EMBL; BC074740; AAH74740.1; -; mRNA. DR CCDS; CCDS33428.1; -. DR PIR; A55737; A55737. DR RefSeq; NP_005009.2; NM_005018.2. DR UniGene; Hs.158297; -. DR PDB; 2M2D; NMR; -; A=34-150. DR PDB; 3RRQ; X-ray; 2.10 A; A=32-160. DR PDB; 4ZQK; X-ray; 2.45 A; B=33-150. DR PDB; 5B8C; X-ray; 2.15 A; C/F/I/L=32-160. DR PDB; 5GGR; X-ray; 3.30 A; Y/Z=26-150. DR PDB; 5GGS; X-ray; 2.00 A; Y/Z=26-148. DR PDB; 5IUS; X-ray; 2.89 A; A/B=26-146. DR PDB; 5JXE; X-ray; 2.90 A; A/B=33-146. DR PDB; 5WT9; X-ray; 2.40 A; G=1-167. DR PDBsum; 2M2D; -. DR PDBsum; 3RRQ; -. DR PDBsum; 4ZQK; -. DR PDBsum; 5B8C; -. DR PDBsum; 5GGR; -. DR PDBsum; 5GGS; -. DR PDBsum; 5IUS; -. DR PDBsum; 5JXE; -. DR PDBsum; 5WT9; -. DR ProteinModelPortal; Q15116; -. DR SMR; Q15116; -. DR BioGrid; 111160; 61. DR DIP; DIP-44126N; -. DR IntAct; Q15116; 5. DR MINT; Q15116; -. DR STRING; 9606.ENSP00000335062; -. DR ChEMBL; CHEMBL3307223; -. DR DrugBank; DB05916; CT-011. DR DrugBank; DB09035; Nivolumab. DR DrugBank; DB09037; Pembrolizumab. DR GuidetoPHARMACOLOGY; 2760; -. DR iPTMnet; Q15116; -. DR PhosphoSitePlus; Q15116; -. DR BioMuta; PDCD1; -. DR DMDM; 145559515; -. DR PaxDb; Q15116; -. DR PeptideAtlas; Q15116; -. DR PRIDE; Q15116; -. DR DNASU; 5133; -. DR Ensembl; ENST00000334409; ENSP00000335062; ENSG00000188389. DR Ensembl; ENST00000618185; ENSP00000480684; ENSG00000276977. DR GeneID; 5133; -. DR KEGG; hsa:5133; -. DR UCSC; uc002wcq.5; human. DR CTD; 5133; -. DR DisGeNET; 5133; -. DR EuPathDB; HostDB:ENSG00000188389.10; -. DR GeneCards; PDCD1; -. DR H-InvDB; HIX0030684; -. DR HGNC; HGNC:8760; PDCD1. DR HPA; CAB038418; -. DR HPA; HPA035981; -. DR MalaCards; PDCD1; -. DR MIM; 109100; phenotype. DR MIM; 600244; gene. DR MIM; 605218; phenotype. DR neXtProt; NX_Q15116; -. DR OpenTargets; ENSG00000188389; -. DR Orphanet; 802; Multiple sclerosis. DR Orphanet; 536; Systemic lupus erythematosus. DR PharmGKB; PA33110; -. DR eggNOG; ENOG410J26W; Eukaryota. DR eggNOG; ENOG41116U6; LUCA. DR GeneTree; ENSGT00390000013662; -. DR HOGENOM; HOG000253959; -. DR HOVERGEN; HBG053534; -. DR InParanoid; Q15116; -. DR KO; K06744; -. DR OMA; DFQWREK; -. DR OrthoDB; EOG091G0EE8; -. DR PhylomeDB; Q15116; -. DR TreeFam; TF336181; -. DR Reactome; R-HSA-389948; PD-1 signaling. DR SIGNOR; Q15116; -. DR ChiTaRS; PDCD1; human. DR GeneWiki; Programmed_cell_death_1; -. DR GenomeRNAi; 5133; -. DR PRO; PR:Q15116; -. DR Proteomes; UP000005640; Chromosome 2. DR Bgee; ENSG00000188389; -. DR CleanEx; HS_PDCD1; -. DR ExpressionAtlas; Q15116; baseline and differential. DR Genevisible; Q15116; HS. DR GO; GO:0009897; C:external side of plasma membrane; IEA:Ensembl. DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW. DR GO; GO:0005886; C:plasma membrane; TAS:Reactome. DR GO; GO:0004871; F:signal transducer activity; TAS:ProtInc. DR GO; GO:0006915; P:apoptotic process; TAS:ProtInc. DR GO; GO:0006959; P:humoral immune response; TAS:ProtInc. DR GO; GO:0007275; P:multicellular organism development; TAS:ProtInc. DR GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl. DR GO; GO:0002644; P:negative regulation of tolerance induction; IEA:Ensembl. DR GO; GO:0070234; P:positive regulation of T cell apoptotic process; IDA:UniProtKB. DR GO; GO:0031295; P:T cell costimulation; TAS:Reactome. DR Gene3D; 2.60.40.10; -; 1. DR InterPro; IPR007110; Ig-like_dom. DR InterPro; IPR036179; Ig-like_dom_sf. DR InterPro; IPR013783; Ig-like_fold. DR InterPro; IPR003599; Ig_sub. DR InterPro; IPR013106; Ig_V-set. DR Pfam; PF07686; V-set; 1. DR SMART; SM00409; IG; 1. DR SMART; SM00406; IGv; 1. DR SUPFAM; SSF48726; SSF48726; 1. DR PROSITE; PS50835; IG_LIKE; 1.|] ftStr :: Text ftStr = [text| FT SIGNAL 1 20 {ECO:0000255}. FT CHAIN 21 288 Programmed cell death protein 1. FT /FTId=PRO_0000014892. FT TOPO_DOM 21 170 Extracellular. {ECO:0000255}. FT TRANSMEM 171 191 Helical. {ECO:0000255}. FT TOPO_DOM 192 288 Cytoplasmic. {ECO:0000255}. FT DOMAIN 35 145 Ig-like V-type. FT CARBOHYD 49 49 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT CARBOHYD 58 58 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT CARBOHYD 74 74 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT CARBOHYD 116 116 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT DISULFID 54 123 {ECO:0000255|PROSITE-ProRule:PRU00114}. FT VARIANT 215 215 A -> V (in dbSNP:rs2227982). FT /FTId=VAR_031685. FT CONFLICT 38 38 S -> F (in Ref. 2; AAC51773). FT {ECO:0000305}. FT CONFLICT 162 162 P -> S (in Ref. 1; AAC41700). FT {ECO:0000305}. FT STRAND 27 29 {ECO:0000244|PDB:5WT9}. FT STRAND 36 38 {ECO:0000244|PDB:5GGS}. FT STRAND 40 45 {ECO:0000244|PDB:5GGS}. FT STRAND 50 55 {ECO:0000244|PDB:5GGS}. FT STRAND 60 70 {ECO:0000244|PDB:5GGS}. FT STRAND 72 74 {ECO:0000244|PDB:4ZQK}. FT STRAND 76 83 {ECO:0000244|PDB:5GGS}. FT STRAND 95 99 {ECO:0000244|PDB:5GGS}. FT STRAND 103 112 {ECO:0000244|PDB:5GGS}. FT HELIX 115 117 {ECO:0000244|PDB:5GGS}. FT STRAND 119 131 {ECO:0000244|PDB:5GGS}. FT STRAND 134 136 {ECO:0000244|PDB:5GGS}. FT STRAND 140 145 {ECO:0000244|PDB:5GGS}.|] sqStr :: Text sqStr = [text| SQ SEQUENCE 288 AA; 31647 MW; A5210FD40C304FB7 CRC64; MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL|] endStr :: Text endStr = "//" pd1Str :: Text pd1Str = [text| ID PDCD1_HUMAN Reviewed; 288 AA. AC Q15116; O00517; Q8IX89; DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot. DT 17-APR-2007, sequence version 3. DT 28-FEB-2018, entry version 163. DE RecName: Full=Programmed cell death protein 1; DE Short=Protein PD-1; DE Short=hPD-1; DE AltName: CD_antigen=CD279; DE Flags: Precursor; GN Name=PDCD1; Synonyms=PD1; OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; OC Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=7851902; DOI=10.1006/geno.1994.1562; RA Shinohara T., Taniwaki M., Ishida Y., Kawaich M., Honjo T.; RT "Structure and chromosomal localization of the human PD-1 gene RT (PDCD1)."; RL Genomics 23:704-706(1994). RN [2] RP NUCLEOTIDE SEQUENCE [MRNA]. RX PubMed=9332365; DOI=10.1016/S0378-1119(97)00260-6; RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R., RA Burrows P.D., Billips L.D.; RT "The human PD-1 gene: complete cDNA, genomic organization, and RT developmentally regulated expression in B cell progenitors."; RL Gene 197:177-187(1997). RN [3] RP ERRATUM. RA Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R., RA Burrows P.D., Billips L.D.; RL Gene 203:253-253(1997). RN [4] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INVOLVEMENT IN SLEB2. RX PubMed=12402038; DOI=10.1038/ng1020; RA Prokunina L., Castillejo-Lopez C., Oberg F., Gunnarsson I., Berg L., RA Magnusson V., Brookes A.J., Tentler D., Kristjansdottir H., RA Grondal G., Bolstad A.I., Svenungsson E., Lundberg I., Sturfelt G., RA Jonssen A., Truedsson L., Lima G., Alcocer-Varela J., Jonsson R., RA Gyllensten U.B., Harley J.B., Alarcon-Segovia D., Steinsson K., RA Alarcon-Riquelme M.E.; RT "A regulatory polymorphism in PDCD1 is associated with susceptibility RT to systemic lupus erythematosus in humans."; RL Nat. Genet. 32:666-669(2002). RN [5] RP NUCLEOTIDE SEQUENCE [MRNA]. RA He X., Xu L., Liu Y., Zeng Y.; RT "Cloning of PD-1 cDNA from activated peripheral leukocytes."; RL Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases. RN [6] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Livingston R.J., Shaffer T., McFarland I., Nguyen C.P., Stanaway I.B., RA Rajkumar N., Johnson E.J., da Ponte S.H., Willa H., Ahearn M.O., RA Bertucci C., Acklestad J., Carroll A., Swanson J., Gildersleeve H.I., RA Nickerson D.A.; RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases. RN [7] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RX PubMed=14702039; DOI=10.1038/ng1285; RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S., RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.; RT "Complete sequencing and characterization of 21,243 full-length human RT cDNAs."; RL Nat. Genet. 36:40-45(2004). RN [8] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RX PubMed=15489334; DOI=10.1101/gr.2596504; RG The MGC Project Team; RT "The status, quality, and expansion of the NIH full-length cDNA RT project: the Mammalian Gene Collection (MGC)."; RL Genome Res. 14:2121-2127(2004). RN [9] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RA Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R., RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., RA Venter J.C.; RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases. RN [10] RP FUNCTION. RX PubMed=21276005; DOI=10.1111/j.1749-6632.2010.05919.x; RA Fife B.T., Pauken K.E.; RT "The role of the PD-1 pathway in autoimmunity and peripheral RT tolerance."; RL Ann. N. Y. Acad. Sci. 1217:45-59(2011). CC -!- FUNCTION: Inhibitory cell surface receptor involved in the CC regulation of T-cell function during immunity and tolerance. Upon CC ligand binding, inhibits T-cell effector functions in an antigen- CC specific manner. Possible cell death inducer, in association with CC other factors. {ECO:0000269|PubMed:21276005}. CC -!- SUBUNIT: Monomer. {ECO:0000250}. CC -!- INTERACTION: CC Q9NZQ7:CD274; NbExp=2; IntAct=EBI-4314328, EBI-4314282; CC Q9NZQ7-1:CD274; NbExp=2; IntAct=EBI-4314328, EBI-15686469; CC Q06124:PTPN11; NbExp=3; IntAct=EBI-4314328, EBI-297779; CC -!- SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane CC protein. CC -!- DEVELOPMENTAL STAGE: Induced at programmed cell death. CC -!- DISEASE: Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A CC chronic, relapsing, inflammatory, and often febrile multisystemic CC disorder of connective tissue, characterized principally by CC involvement of the skin, joints, kidneys and serosal membranes. It CC is of unknown etiology, but is thought to represent a failure of CC the regulatory mechanisms of the autoimmune system. The disease is CC marked by a wide range of system dysfunctions, an elevated CC erythrocyte sedimentation rate, and the formation of LE cells in CC the blood or bone marrow. {ECO:0000269|PubMed:12402038}. CC Note=Disease susceptibility is associated with variations CC affecting the gene represented in this entry. DR EMBL; L27440; AAC41700.1; -; Genomic_DNA. DR EMBL; U64863; AAC51773.1; -; mRNA. DR EMBL; AF363458; AAN64003.1; -; Genomic_DNA. DR EMBL; AY238517; AAO63583.1; -; mRNA. DR EMBL; EF064716; ABK41899.1; -; Genomic_DNA. DR EMBL; AK313848; BAG36577.1; -; mRNA. DR EMBL; CH471063; EAW71298.1; -; Genomic_DNA. DR EMBL; BC074740; AAH74740.1; -; mRNA. DR CCDS; CCDS33428.1; -. DR PIR; A55737; A55737. DR RefSeq; NP_005009.2; NM_005018.2. DR UniGene; Hs.158297; -. DR PDB; 2M2D; NMR; -; A=34-150. DR PDB; 3RRQ; X-ray; 2.10 A; A=32-160. DR PDB; 4ZQK; X-ray; 2.45 A; B=33-150. DR PDB; 5B8C; X-ray; 2.15 A; C/F/I/L=32-160. DR PDB; 5GGR; X-ray; 3.30 A; Y/Z=26-150. DR PDB; 5GGS; X-ray; 2.00 A; Y/Z=26-148. DR PDB; 5IUS; X-ray; 2.89 A; A/B=26-146. DR PDB; 5JXE; X-ray; 2.90 A; A/B=33-146. DR PDB; 5WT9; X-ray; 2.40 A; G=1-167. DR PDBsum; 2M2D; -. DR PDBsum; 3RRQ; -. DR PDBsum; 4ZQK; -. DR PDBsum; 5B8C; -. DR PDBsum; 5GGR; -. DR PDBsum; 5GGS; -. DR PDBsum; 5IUS; -. DR PDBsum; 5JXE; -. DR PDBsum; 5WT9; -. DR ProteinModelPortal; Q15116; -. DR SMR; Q15116; -. DR BioGrid; 111160; 61. DR DIP; DIP-44126N; -. DR IntAct; Q15116; 5. DR MINT; Q15116; -. DR STRING; 9606.ENSP00000335062; -. DR ChEMBL; CHEMBL3307223; -. DR DrugBank; DB05916; CT-011. DR DrugBank; DB09035; Nivolumab. DR DrugBank; DB09037; Pembrolizumab. DR GuidetoPHARMACOLOGY; 2760; -. DR iPTMnet; Q15116; -. DR PhosphoSitePlus; Q15116; -. DR BioMuta; PDCD1; -. DR DMDM; 145559515; -. DR PaxDb; Q15116; -. DR PeptideAtlas; Q15116; -. DR PRIDE; Q15116; -. DR DNASU; 5133; -. DR Ensembl; ENST00000334409; ENSP00000335062; ENSG00000188389. DR Ensembl; ENST00000618185; ENSP00000480684; ENSG00000276977. DR GeneID; 5133; -. DR KEGG; hsa:5133; -. DR UCSC; uc002wcq.5; human. DR CTD; 5133; -. DR DisGeNET; 5133; -. DR EuPathDB; HostDB:ENSG00000188389.10; -. DR GeneCards; PDCD1; -. DR H-InvDB; HIX0030684; -. DR HGNC; HGNC:8760; PDCD1. DR HPA; CAB038418; -. DR HPA; HPA035981; -. DR MalaCards; PDCD1; -. DR MIM; 109100; phenotype. DR MIM; 600244; gene. DR MIM; 605218; phenotype. DR neXtProt; NX_Q15116; -. DR OpenTargets; ENSG00000188389; -. DR Orphanet; 802; Multiple sclerosis. DR Orphanet; 536; Systemic lupus erythematosus. DR PharmGKB; PA33110; -. DR eggNOG; ENOG410J26W; Eukaryota. DR eggNOG; ENOG41116U6; LUCA. DR GeneTree; ENSGT00390000013662; -. DR HOGENOM; HOG000253959; -. DR HOVERGEN; HBG053534; -. DR InParanoid; Q15116; -. DR KO; K06744; -. DR OMA; DFQWREK; -. DR OrthoDB; EOG091G0EE8; -. DR PhylomeDB; Q15116; -. DR TreeFam; TF336181; -. DR Reactome; R-HSA-389948; PD-1 signaling. DR SIGNOR; Q15116; -. DR ChiTaRS; PDCD1; human. DR GeneWiki; Programmed_cell_death_1; -. DR GenomeRNAi; 5133; -. DR PRO; PR:Q15116; -. DR Proteomes; UP000005640; Chromosome 2. DR Bgee; ENSG00000188389; -. DR CleanEx; HS_PDCD1; -. DR ExpressionAtlas; Q15116; baseline and differential. DR Genevisible; Q15116; HS. DR GO; GO:0009897; C:external side of plasma membrane; IEA:Ensembl. DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW. DR GO; GO:0005886; C:plasma membrane; TAS:Reactome. DR GO; GO:0004871; F:signal transducer activity; TAS:ProtInc. DR GO; GO:0006915; P:apoptotic process; TAS:ProtInc. DR GO; GO:0006959; P:humoral immune response; TAS:ProtInc. DR GO; GO:0007275; P:multicellular organism development; TAS:ProtInc. DR GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl. DR GO; GO:0002644; P:negative regulation of tolerance induction; IEA:Ensembl. DR GO; GO:0070234; P:positive regulation of T cell apoptotic process; IDA:UniProtKB. DR GO; GO:0031295; P:T cell costimulation; TAS:Reactome. DR Gene3D; 2.60.40.10; -; 1. DR InterPro; IPR007110; Ig-like_dom. DR InterPro; IPR036179; Ig-like_dom_sf. DR InterPro; IPR013783; Ig-like_fold. DR InterPro; IPR003599; Ig_sub. DR InterPro; IPR013106; Ig_V-set. DR Pfam; PF07686; V-set; 1. DR SMART; SM00409; IG; 1. DR SMART; SM00406; IGv; 1. DR SUPFAM; SSF48726; SSF48726; 1. DR PROSITE; PS50835; IG_LIKE; 1. PE 1: Evidence at protein level; KW 3D-structure; Apoptosis; Complete proteome; Disulfide bond; KW Glycoprotein; Immunity; Immunoglobulin domain; Membrane; Polymorphism; KW Reference proteome; Signal; Systemic lupus erythematosus; KW Transmembrane; Transmembrane helix. FT SIGNAL 1 20 {ECO:0000255}. FT CHAIN 21 288 Programmed cell death protein 1. FT /FTId=PRO_0000014892. FT TOPO_DOM 21 170 Extracellular. {ECO:0000255}. FT TRANSMEM 171 191 Helical. {ECO:0000255}. FT TOPO_DOM 192 288 Cytoplasmic. {ECO:0000255}. FT DOMAIN 35 145 Ig-like V-type. FT CARBOHYD 49 49 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT CARBOHYD 58 58 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT CARBOHYD 74 74 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT CARBOHYD 116 116 N-linked (GlcNAc...) asparagine. FT {ECO:0000255}. FT DISULFID 54 123 {ECO:0000255|PROSITE-ProRule:PRU00114}. FT VARIANT 215 215 A -> V (in dbSNP:rs2227982). FT /FTId=VAR_031685. FT CONFLICT 38 38 S -> F (in Ref. 2; AAC51773). FT {ECO:0000305}. FT CONFLICT 162 162 P -> S (in Ref. 1; AAC41700). FT {ECO:0000305}. FT STRAND 27 29 {ECO:0000244|PDB:5WT9}. FT STRAND 36 38 {ECO:0000244|PDB:5GGS}. FT STRAND 40 45 {ECO:0000244|PDB:5GGS}. FT STRAND 50 55 {ECO:0000244|PDB:5GGS}. FT STRAND 60 70 {ECO:0000244|PDB:5GGS}. FT STRAND 72 74 {ECO:0000244|PDB:4ZQK}. FT STRAND 76 83 {ECO:0000244|PDB:5GGS}. FT STRAND 95 99 {ECO:0000244|PDB:5GGS}. FT STRAND 103 112 {ECO:0000244|PDB:5GGS}. FT HELIX 115 117 {ECO:0000244|PDB:5GGS}. FT STRAND 119 131 {ECO:0000244|PDB:5GGS}. FT STRAND 134 136 {ECO:0000244|PDB:5GGS}. FT STRAND 140 145 {ECO:0000244|PDB:5GGS}. SQ SEQUENCE 288 AA; 31647 MW; A5210FD40C304FB7 CRC64; MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL //|] idAns :: ID idAns = ID "PDCD1_HUMAN" Reviewed 288 acAns :: AC acAns = AC ["Q15116", "O00517", "Q8IX89"] dtAns :: DT dtAns = DT "01-NOV-1997" "Swiss-Prot" "17-APR-2007" 3 "28-FEB-2018" 163 deAns :: DE deAns = DE (Just (Name "Programmed cell death protein 1" ["Protein PD-1", "hPD-1"] [])) [CDAntigen "CD279"] [] [] [] [Precursor] de2Ans :: DE de2Ans = DE (Just (Name "Arginine biosynthesis bifunctional protein argJ" [] [])) [] [] [DE (Just (Name "Glutamate N-acetyltransferase" [] ["2.3.1.35"])) [Simple (Name "Ornithine acetyltransferase" ["OATase"] []), Simple (Name "Ornithine transacetylase" [] [])] [] [] [] [], DE (Just (Name "Amino-acid acetyltransferase" [] ["2.3.1.1"])) [Simple (Name "N-acetylglutamate synthase" ["AGS"] [])] [] [] [] [] ] [DE (Just (Name "Arginine biosynthesis bifunctional protein argJ alpha chain" [] [])) [] [] [] [] [], DE (Just (Name "Arginine biosynthesis bifunctional protein argJ beta chain" [] [])) [] [] [] [] []] [] gnAns :: [GN] gnAns = [GN (Just "PDCD1") ["PD1"] [] []] osAns :: OS osAns = OS "Homo sapiens (Human)" ogAns :: OG ogAns = Plasmid ["R6-5", "IncFII R100 (NR1)", "IncFII R1-19 (R1 drd-19)"] ocAns :: OC ocAns = OC ["Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini", "Hominidae", "Homo"] ohAns :: OH ohAns = OH "9536" "Cercopithecus hamlyni (Owl-faced monkey) (Hamlyn's monkey)" oxAns :: OX oxAns = OX "NCBI_TaxID" "9606" refAns :: [Reference] refAns = [Reference 1 "NUCLEOTIDE SEQUENCE [GENOMIC DNA]" [] [(PubMed,"7851902"),(DOI,"10.1006/geno.1994.1562")] [] ["Shinohara T.","Taniwaki M.","Ishida Y.","Kawaich M.","Honjo T."] (Just "Structure and chromosomal localization of the human PD-1 gene (PDCD1).") "Genomics 23:704-706(1994)", Reference 2 "NUCLEOTIDE SEQUENCE [MRNA]" [] [(PubMed,"9332365"),(DOI,"10.1016/S0378-1119(97)00260-6")] [] ["Finger L.R.","Pu J.","Wasserman R.","Vibhakar R.","Louie E.","Hardy R.R.","Burrows P.D.","Billips L.D."] (Just "The human PD-1 gene: complete cDNA, genomic organization, and developmentally regulated expression in B cell progenitors.") "Gene 197:177-187(1997)", Reference 3 "ERRATUM" [] [] [] ["Finger L.R.","Pu J.","Wasserman R.","Vibhakar R.","Louie E.","Hardy R.R.","Burrows P.D.","Billips L.D."] Nothing "Gene 203:253-253(1997)", Reference 4 "NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INVOLVEMENT IN SLEB2" [] [(PubMed,"12402038"),(DOI,"10.1038/ng1020")] [] ["Prokunina L.","Castillejo-Lopez C.","Oberg F.","Gunnarsson I.","Berg L.","Magnusson V.","Brookes A.J.","Tentler D.","Kristjansdottir H.","Grondal G.","Bolstad A.I.","Svenungsson E.","Lundberg I.","Sturfelt G.","Jonssen A.","Truedsson L.","Lima G.","Alcocer-Varela J.","Jonsson R.","Gyllensten U.B.","Harley J.B.","Alarcon-Segovia D.","Steinsson K.","Alarcon-Riquelme M.E."] (Just "A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans.") "Nat. Genet. 32:666-669(2002)", Reference 5 "NUCLEOTIDE SEQUENCE [MRNA]" [] [] [] ["He X.","Xu L.","Liu Y.","Zeng Y."] (Just "Cloning of PD-1 cDNA from activated peripheral leukocytes.") "Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases", Reference 6 "NUCLEOTIDE SEQUENCE [GENOMIC DNA]" [] [] [] ["Livingston R.J.","Shaffer T.","McFarland I.","Nguyen C.P.","Stanaway I.B.","Rajkumar N.","Johnson E.J.","da Ponte S.H.","Willa H.","Ahearn M.O.","Bertucci C.","Acklestad J.","Carroll A.","Swanson J.","Gildersleeve H.I.","Nickerson D.A."] Nothing "Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases", Reference 7 "NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]" [] [(PubMed,"14702039"),(DOI,"10.1038/ng1285")] [] ["Ota T.","Suzuki Y.","Nishikawa T.","Otsuki T.","Sugiyama T.","Irie R.","Wakamatsu A.","Hayashi K.","Sato H.","Nagai K.","Kimura K.","Makita H.","Sekine M.","Obayashi M.","Nishi T.","Shibahara T.","Tanaka T.","Ishii S.","Yamamoto J.","Saito K.","Kawai Y.","Isono Y.","Nakamura Y.","Nagahari K.","Murakami K.","Yasuda T.","Iwayanagi T.","Wagatsuma M.","Shiratori A.","Sudo H.","Hosoiri T.","Kaku Y.","Kodaira H.","Kondo H.","Sugawara M.","Takahashi M.","Kanda K.","Yokoi T.","Furuya T.","Kikkawa E.","Omura Y.","Abe K.","Kamihara K.","Katsuta N.","Sato K.","Tanikawa M.","Yamazaki M.","Ninomiya K.","Ishibashi T.","Yamashita H.","Murakawa K.","Fujimori K.","Tanai H.","Kimata M.","Watanabe M.","Hiraoka S.","Chiba Y.","Ishida S.","Ono Y.","Takiguchi S.","Watanabe S.","Yosida M.","Hotuta T.","Kusano J.","Kanehori K.","Takahashi-Fujii A.","Hara H.","Tanase T.-O.","Nomura Y.","Togiya S.","Komai F.","Hara R.","Takeuchi K.","Arita M.","Imose N.","Musashino K.","Yuuki H.","Oshima A.","Sasaki N.","Aotsuka S.","Yoshikawa Y.","Matsunawa H.","Ichihara T.","Shiohata N.","Sano S.","Moriya S.","Momiyama H.","Satoh N.","Takami S.","Terashima Y.","Suzuki O.","Nakagawa S.","Senoh A.","Mizoguchi H.","Goto Y.","Shimizu F.","Wakebe H.","Hishigaki H.","Watanabe T.","Sugiyama A.","Takemoto M.","Kawakami B.","Yamazaki M.","Watanabe K.","Kumagai A.","Itakura S.","Fukuzumi Y.","Fujimori Y.","Komiyama M.","Tashiro H.","Tanigami A.","Fujiwara T.","Ono T.","Yamada K.","Fujii Y.","Ozaki K.","Hirao M.","Ohmori Y.","Kawabata A.","Hikiji T.","Kobatake N.","Inagaki H.","Ikema Y.","Okamoto S.","Okitani R.","Kawakami T.","Noguchi S.","Itoh T.","Shigeta K.","Senba T.","Matsumura K.","Nakajima Y.","Mizuno T.","Morinaga M.","Sasaki M.","Togashi T.","Oyama M.","Hata H.","Watanabe M.","Komatsu T.","Mizushima-Sugano J.","Satoh T.","Shirai Y.","Takahashi Y.","Nakagawa K.","Okumura K.","Nagase T.","Nomura N.","Kikuchi H.","Masuho Y.","Yamashita R.","Nakai K.","Yada T.","Nakamura Y.","Ohara O.","Isogai T.","Sugano S."] (Just "Complete sequencing and characterization of 21,243 full-length human cDNAs.") "Nat. Genet. 36:40-45(2004)", Reference 8 "NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]" [] [(PubMed,"15489334"),(DOI,"10.1101/gr.2596504")] ["The MGC Project Team;"] [] (Just "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).") "Genome Res. 14:2121-2127(2004)", Reference 9 "NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]" [] [] [] ["Mural R.J.","Istrail S.","Sutton G.","Florea L.","Halpern A.L.","Mobarry C.M.","Lippert R.","Walenz B.","Shatkay H.","Dew I.","Miller J.R.","Flanigan M.J.","Edwards N.J.","Bolanos R.","Fasulo D.","Halldorsson B.V.","Hannenhalli S.","Turner R.","Yooseph S.","Lu F.","Nusskern D.R.","Shue B.C.","Zheng X.H.","Zhong F.","Delcher A.L.","Huson D.H.","Kravitz S.A.","Mouchard L.","Reinert K.","Remington K.A.","Clark A.G.","Waterman M.S.","Eichler E.E.","Adams M.D.","Hunkapiller M.W.","Myers E.W.","Venter J.C."] Nothing "Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases", Reference 10 "FUNCTION" [] [(PubMed,"21276005"),(DOI,"10.1111/j.1749-6632.2010.05919.x")] [] ["Fife B.T.","Pauken K.E."] (Just "The role of the PD-1 pathway in autoimmunity and peripheral tolerance.") "Ann. N. Y. Acad. Sci. 1217:45-59(2011)"] ccAns :: [CC] ccAns = [CC "FUNCTION" "Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.", CC "SUBUNIT" "Monomer.", CC "INTERACTION" "Q9NZQ7:CD274; NbExp=2; IntAct=EBI-4314328, EBI-4314282; Q9NZQ7-1:CD274; NbExp=2; IntAct=EBI-4314328, EBI-15686469; Q06124:PTPN11; NbExp=3; IntAct=EBI-4314328, EBI-297779;", CC "SUBCELLULAR LOCATION" "Membrane; Single-pass type I membrane protein.", CC "DEVELOPMENTAL STAGE" "Induced at programmed cell death.", CC "DISEASE" "Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow."] drAns :: [DR] drAns = [DR "EMBL" "L27440" ["AAC41700.1","-","Genomic_DNA"], DR "EMBL" "U64863" ["AAC51773.1","-","mRNA"], DR "EMBL" "AF363458" ["AAN64003.1","-","Genomic_DNA"], DR "EMBL" "AY238517" ["AAO63583.1","-","mRNA"], DR "EMBL" "EF064716" ["ABK41899.1","-","Genomic_DNA"], DR "EMBL" "AK313848" ["BAG36577.1","-","mRNA"], DR "EMBL" "CH471063" ["EAW71298.1","-","Genomic_DNA"], DR "EMBL" "BC074740" ["AAH74740.1","-","mRNA"], DR "CCDS" "CCDS33428.1" ["-"], DR "PIR" "A55737" ["A55737"], DR "RefSeq" "NP_005009.2" ["NM_005018.2"], DR "UniGene" "Hs.158297" ["-"], DR "PDB" "2M2D" ["NMR","-","A=34-150"], DR "PDB" "3RRQ" ["X-ray","2.10 A","A=32-160"], DR "PDB" "4ZQK" ["X-ray","2.45 A","B=33-150"], DR "PDB" "5B8C" ["X-ray","2.15 A","C/F/I/L=32-160"], DR "PDB" "5GGR" ["X-ray","3.30 A","Y/Z=26-150"], DR "PDB" "5GGS" ["X-ray","2.00 A","Y/Z=26-148"], DR "PDB" "5IUS" ["X-ray","2.89 A","A/B=26-146"], DR "PDB" "5JXE" ["X-ray","2.90 A","A/B=33-146"], DR "PDB" "5WT9" ["X-ray","2.40 A","G=1-167"], DR "PDBsum" "2M2D" ["-"], DR "PDBsum" "3RRQ" ["-"], DR "PDBsum" "4ZQK" ["-"], DR "PDBsum" "5B8C" ["-"], DR "PDBsum" "5GGR" ["-"], DR "PDBsum" "5GGS" ["-"], DR "PDBsum" "5IUS" ["-"], DR "PDBsum" "5JXE" ["-"], DR "PDBsum" "5WT9" ["-"], DR "ProteinModelPortal" "Q15116" ["-"], DR "SMR" "Q15116" ["-"], DR "BioGrid" "111160" ["61"], DR "DIP" "DIP-44126N" ["-"], DR "IntAct" "Q15116" ["5"], DR "MINT" "Q15116" ["-"], DR "STRING" "9606.ENSP00000335062" ["-"], DR "ChEMBL" "CHEMBL3307223" ["-"], DR "DrugBank" "DB05916" ["CT-011"], DR "DrugBank" "DB09035" ["Nivolumab"], DR "DrugBank" "DB09037" ["Pembrolizumab"], DR "GuidetoPHARMACOLOGY" "2760" ["-"], DR "iPTMnet" "Q15116" ["-"], DR "PhosphoSitePlus" "Q15116" ["-"], DR "BioMuta" "PDCD1" ["-"], DR "DMDM" "145559515" ["-"], DR "PaxDb" "Q15116" ["-"], DR "PeptideAtlas" "Q15116" ["-"], DR "PRIDE" "Q15116" ["-"], DR "DNASU" "5133" ["-"], DR "Ensembl" "ENST00000334409" ["ENSP00000335062","ENSG00000188389"], DR "Ensembl" "ENST00000618185" ["ENSP00000480684","ENSG00000276977"], DR "GeneID" "5133" ["-"], DR "KEGG" "hsa:5133" ["-"], DR "UCSC" "uc002wcq.5" ["human"], DR "CTD" "5133" ["-"], DR "DisGeNET" "5133" ["-"], DR "EuPathDB" "HostDB:ENSG00000188389.10" ["-"], DR "GeneCards" "PDCD1" ["-"], DR "H-InvDB" "HIX0030684" ["-"], DR "HGNC" "HGNC:8760" ["PDCD1"], DR "HPA" "CAB038418" ["-"], DR "HPA" "HPA035981" ["-"], DR "MalaCards" "PDCD1" ["-"], DR "MIM" "109100" ["phenotype"], DR "MIM" "600244" ["gene"], DR "MIM" "605218" ["phenotype"], DR "neXtProt" "NX_Q15116" ["-"], DR "OpenTargets" "ENSG00000188389" ["-"], DR "Orphanet" "802" ["Multiple sclerosis"], DR "Orphanet" "536" ["Systemic lupus erythematosus"], DR "PharmGKB" "PA33110" ["-"], DR "eggNOG" "ENOG410J26W" ["Eukaryota"], DR "eggNOG" "ENOG41116U6" ["LUCA"], DR "GeneTree" "ENSGT00390000013662" ["-"], DR "HOGENOM" "HOG000253959" ["-"], DR "HOVERGEN" "HBG053534" ["-"], DR "InParanoid" "Q15116" ["-"], DR "KO" "K06744" ["-"], DR "OMA" "DFQWREK" ["-"], DR "OrthoDB" "EOG091G0EE8" ["-"], DR "PhylomeDB" "Q15116" ["-"], DR "TreeFam" "TF336181" ["-"], DR "Reactome" "R-HSA-389948" ["PD-1 signaling"], DR "SIGNOR" "Q15116" ["-"], DR "ChiTaRS" "PDCD1" ["human"], DR "GeneWiki" "Programmed_cell_death_1" ["-"], DR "GenomeRNAi" "5133" ["-"], DR "PRO" "PR:Q15116" ["-"], DR "Proteomes" "UP000005640" ["Chromosome 2"], DR "Bgee" "ENSG00000188389" ["-"], DR "CleanEx" "HS_PDCD1" ["-"], DR "ExpressionAtlas" "Q15116" ["baseline and differential"], DR "Genevisible" "Q15116" ["HS"], DR "GO" "GO:0009897" ["C:external side of plasma membrane","IEA:Ensembl"], DR "GO" "GO:0016021" ["C:integral component of membrane","IEA:UniProtKB-KW"], DR "GO" "GO:0005886" ["C:plasma membrane","TAS:Reactome"], DR "GO" "GO:0004871" ["F:signal transducer activity","TAS:ProtInc"], DR "GO" "GO:0006915" ["P:apoptotic process","TAS:ProtInc"], DR "GO" "GO:0006959" ["P:humoral immune response","TAS:ProtInc"], DR "GO" "GO:0007275" ["P:multicellular organism development","TAS:ProtInc"], DR "GO" "GO:0043066" ["P:negative regulation of apoptotic process","IEA:Ensembl"], DR "GO" "GO:0002644" ["P:negative regulation of tolerance induction","IEA:Ensembl"], DR "GO" "GO:0070234" ["P:positive regulation of T cell apoptotic process","IDA:UniProtKB"], DR "GO" "GO:0031295" ["P:T cell costimulation","TAS:Reactome"], DR "Gene3D" "2.60.40.10" ["-","1"], DR "InterPro" "IPR007110" ["Ig-like_dom"], DR "InterPro" "IPR036179" ["Ig-like_dom_sf"], DR "InterPro" "IPR013783" ["Ig-like_fold"], DR "InterPro" "IPR003599" ["Ig_sub"], DR "InterPro" "IPR013106" ["Ig_V-set"], DR "Pfam" "PF07686" ["V-set","1"], DR "SMART" "SM00409" ["IG","1"], DR "SMART" "SM00406" ["IGv","1"], DR "SUPFAM" "SSF48726" ["SSF48726","1"], DR "PROSITE" "PS50835" ["IG_LIKE","1"]] peAns :: PE peAns = EvidenceAtProteinLevel kwAns :: KW kwAns = KW ["3D-structure", "Apoptosis", "Complete proteome", "Disulfide bond", "Glycoprotein", "Immunity", "Immunoglobulin domain", "Membrane", "Polymorphism", "Reference proteome", "Signal", "Systemic lupus erythematosus", "Transmembrane", "Transmembrane helix"] ftAns :: [FT] ftAns = [FT "SIGNAL" (ExactEP 1) (ExactEP 20) [], FT "CHAIN" (ExactEP 21) (ExactEP 288) ["Programmed cell death protein 1","/FTId=PRO_0000014892"], FT "TOPO_DOM" (ExactEP 21) (ExactEP 170) ["Extracellular"], FT "TRANSMEM" (ExactEP 171) (ExactEP 191) ["Helical"], FT "TOPO_DOM" (ExactEP 192) (ExactEP 288) ["Cytoplasmic"], FT "DOMAIN" (ExactEP 35) (ExactEP 145) ["Ig-like V-type"], FT "CARBOHYD" (ExactEP 49) (ExactEP 49) ["N-linked (GlcNAc...) asparagine"], FT "CARBOHYD" (ExactEP 58) (ExactEP 58) ["N-linked (GlcNAc...) asparagine"], FT "CARBOHYD" (ExactEP 74) (ExactEP 74) ["N-linked (GlcNAc...) asparagine"], FT "CARBOHYD" (ExactEP 116) (ExactEP 116) ["N-linked (GlcNAc...) asparagine"], FT "DISULFID" (ExactEP 54) (ExactEP 123) [], FT "VARIANT" (ExactEP 215) (ExactEP 215) ["A -> V (in dbSNP:rs2227982)","/FTId=VAR_031685"], FT "CONFLICT" (ExactEP 38) (ExactEP 38) ["S -> F (in Ref. 2; AAC51773)"], FT "CONFLICT" (ExactEP 162) (ExactEP 162) ["P -> S (in Ref. 1; AAC41700)"], FT "STRAND" (ExactEP 27) (ExactEP 29) [], FT "STRAND" (ExactEP 36) (ExactEP 38) [], FT "STRAND" (ExactEP 40) (ExactEP 45) [], FT "STRAND" (ExactEP 50) (ExactEP 55) [], FT "STRAND" (ExactEP 60) (ExactEP 70) [], FT "STRAND" (ExactEP 72) (ExactEP 74) [], FT "STRAND" (ExactEP 76) (ExactEP 83) [], FT "STRAND" (ExactEP 95) (ExactEP 99) [], FT "STRAND" (ExactEP 103) (ExactEP 112) [], FT "HELIX" (ExactEP 115) (ExactEP 117) [], FT "STRAND" (ExactEP 119) (ExactEP 131) [], FT "STRAND" (ExactEP 134) (ExactEP 136) [], FT "STRAND" (ExactEP 140) (ExactEP 145) []] sqAns :: SQ sqAns = SQ 288 31647 "A5210FD40C304FB7" "MQIPQAPWPVVWAVLQLGWRPGWFLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVVGVVGGLLGSLVLLVWVLAVICSRAARGTIGARRTGQPLKEDPSAVPVFSVDYGELDFQWREKTPEPPVPCVPEQTEYATIVFPSGMGTSSPARRGSADGPRSAQPLRPEDGHCSWPL" endAns :: () endAns = () main :: IO () main = hspec $ do describe "Parse individual sections" $ do it "parses ID lines" $ parseOnly parseID idStr `shouldBe` Right idAns it "parses AC lines" $ parseOnly parseAC acStr `shouldBe` Right acAns it "parses DT lines" $ parseOnly parseDT dtStr `shouldBe` Right dtAns it "parses DE lines" $ do parseOnly parseDE deStr `shouldBe` Right deAns parseOnly parseDE de2Str `shouldBe` Right de2Ans it "parses GN lines" $ parseOnly parseGN gnStr `shouldBe` Right gnAns it "parses OS lines" $ parseOnly parseOS osStr `shouldBe` Right osAns it "parses OG lines (non-PD1)" $ parseOnly parseOG ogStr `shouldBe` Right ogAns it "parses OC lines" $ parseOnly parseOC ocStr `shouldBe` Right ocAns it "parses OX lines (non-PD1)" $ parseOnly parseOX oxStr `shouldBe` Right oxAns it "parses OH lines (non-PD1)" $ parseOnly parseOH ohStr `shouldBe` Right ohAns it "parses REF lines" $ do let parseManyRef = (:) <$> parseRef <*> many' (endOfLine *> parseRef) parseOnly parseManyRef refStr `shouldBe` Right refAns it "parses CC lines" $ do let parseManyCC = (:) <$> parseCC <*> many' (endOfLine *> parseCC) parseOnly parseManyCC ccStr `shouldBe` Right ccAns it "parses DR lines" $ do let parseManyDR = (:) <$> parseDR <*> many' (endOfLine *> parseDR) parseOnly parseManyDR drStr `shouldBe` Right drAns it "parses PE lines" $ parseOnly parsePE peStr `shouldBe` Right peAns it "parses KW lines" $ parseOnly parseKW kwStr `shouldBe` Right kwAns it "parses FT lines" $ do let parseManyFT = (:) <$> parseFT <*> many' (endOfLine *> parseFT) parseOnly parseManyFT ftStr `shouldBe` Right ftAns it "parses SQ lines" $ do parseOnly parseSQ sqStr `shouldBe` Right sqAns it "parses End lines" $ parseOnly parseEnd endStr `shouldBe` Right endAns describe "Parse Record" $ do it "parses PD1 example" $ do let record = Record idAns acAns dtAns deAns gnAns osAns [] ocAns oxAns [] refAns ccAns drAns peAns (Just kwAns) ftAns sqAns parseOnly parseRecord pd1Str `shouldBe` Right record