ID   VSIG4_HUMAN             Reviewed;         399 AA.
AC   Q9Y279; Q6UXI4;
DT   15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1999, sequence version 1.
DT   27-MAR-2024, entry version 187.
DE   RecName: Full=V-set and immunoglobulin domain-containing protein 4;
DE   AltName: Full=Protein Z39Ig;
DE   Flags: Precursor;
GN   Name=VSIG4; Synonyms=CRIg, Z39IG; ORFNames=UNQ317/PRO362;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND TISSUE SPECIFICITY.
RX   PubMed=11004523; DOI=10.1016/s0167-4781(00)00131-7;
RA   Langnaese K., Colleaux L., Kloos D.U., Fontes M., Wieacker P.;
RT   "Cloning of Z39Ig, a novel gene with immunoglobulin-like domains located on
RT   human chromosome X.";
RL   Biochim. Biophys. Acta 1492:522-525(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RX   PubMed=12975309; DOI=10.1101/gr.1293003;
RA   Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J.,
RA   Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P.,
RA   Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E., Heldens S., Huang A.,
RA   Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D.,
RA   Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L.,
RA   Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C.,
RA   Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J.,
RA   Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.;
RT   "The secreted protein discovery initiative (SPDI), a large-scale effort to
RT   identify novel human secreted and transmembrane proteins: a bioinformatics
RT   assessment.";
RL   Genome Res. 13:2265-2270(2003).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC   TISSUE=Placenta;
RA   Li W.B., Gruber C., Jessee J., Polayes D.;
RT   "Full-length cDNA libraries and normalization.";
RL   Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=15772651; DOI=10.1038/nature03440;
RA   Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D.,
RA   Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L.,
RA   Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.,
RA   Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A.,
RA   Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P.,
RA   Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D.,
RA   Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D.,
RA   Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L.,
RA   Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P.,
RA   Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G.,
RA   Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J.,
RA   Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D.,
RA   Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L.,
RA   Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z.,
RA   Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S.,
RA   Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S.,
RA   Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O.,
RA   Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H.,
RA   Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T.,
RA   Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L.,
RA   Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R.,
RA   Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y.,
RA   Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K.,
RA   Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J.,
RA   Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L.,
RA   Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S.,
RA   Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A.,
RA   Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L.,
RA   Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D.,
RA   Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H.,
RA   McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S.,
RA   Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C.,
RA   Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S.,
RA   Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V.,
RA   Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K.,
RA   Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K.,
RA   Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D.,
RA   Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R.,
RA   Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B.,
RA   Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C.,
RA   d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q.,
RA   Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N.,
RA   Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A.,
RA   Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J.,
RA   Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A.,
RA   Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F.,
RA   Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L.,
RA   Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S.,
RA   Rogers J., Bentley D.R.;
RT   "The DNA sequence of the human X chromosome.";
RL   Nature 434:325-337(2005).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   TISSUE=Brain;
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 project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [6]
RP   PROTEIN SEQUENCE OF 20-34.
RX   PubMed=15340161; DOI=10.1110/ps.04682504;
RA   Zhang Z., Henzel W.J.;
RT   "Signal peptide prediction based on analysis of experimentally verified
RT   cleavage sites.";
RL   Protein Sci. 13:2819-2824(2004).
RN   [7]
RP   FUNCTION, AND TISSUE SPECIFICITY.
RX   PubMed=17016562; DOI=10.1172/jci25673;
RA   Vogt L., Schmitz N., Kurrer M.O., Bauer M., Hinton H.I., Behnke S.,
RA   Gatto D., Sebbel P., Beerli R.R., Sonderegger I., Kopf M., Saudan P.,
RA   Bachmann M.F.;
RT   "VSIG4, a B7 family-related protein, is a negative regulator of T cell
RT   activation.";
RL   J. Clin. Invest. 116:2817-2826(2006).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF 19-137 IN COMPLEX WITH C3B AND
RP   C3C, FUNCTION, AND DISULFIDE BOND.
RX   PubMed=17051150; DOI=10.1038/nature05263;
RA   Wiesmann C., Katschke K.J., Yin J., Helmy K.Y., Steffek M.,
RA   Fairbrother W.J., McCallum S.A., Embuscado L., DeForge L., Hass P.E.,
RA   van Lookeren Campagne M.;
RT   "Structure of C3b in complex with CRIg gives insights into regulation of
RT   complement activation.";
RL   Nature 444:217-220(2006).
CC   -!- FUNCTION: Phagocytic receptor, strong negative regulator of T-cell
CC       proliferation and IL2 production. Potent inhibitor of the alternative
CC       complement pathway convertases. {ECO:0000269|PubMed:17016562,
CC       ECO:0000269|PubMed:17051150}.
CC   -!- INTERACTION:
CC       Q9Y279; Q969F0: FATE1; NbExp=3; IntAct=EBI-903131, EBI-743099;
CC       Q9Y279; Q8N5M9: JAGN1; NbExp=3; IntAct=EBI-903131, EBI-10266796;
CC       Q9Y279; O95183: VAMP5; NbExp=3; IntAct=EBI-903131, EBI-10191195;
CC       Q9Y279-1; P01024: C3; NbExp=5; IntAct=EBI-903144, EBI-905851;
CC       Q9Y279-2; P01024: C3; NbExp=2; IntAct=EBI-903148, EBI-905851;
CC   -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass type I
CC       membrane protein {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1;
CC         IsoId=Q9Y279-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9Y279-2; Sequence=VSP_012813;
CC       Name=3;
CC         IsoId=Q9Y279-3; Sequence=VSP_041213;
CC   -!- TISSUE SPECIFICITY: Abundantly expressed in several fetal tissues. In
CC       adult tissues, highest expression in lung and placenta. Expressed in
CC       resting macrophages. {ECO:0000269|PubMed:11004523,
CC       ECO:0000269|PubMed:17016562}.
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DR   EMBL; AJ132502; CAB51536.1; -; mRNA.
DR   EMBL; AY358341; AAQ88707.1; -; mRNA.
DR   EMBL; AL034397; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CR607860; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; BC010525; AAH10525.1; -; mRNA.
DR   CCDS; CCDS14383.1; -. [Q9Y279-1]
DR   CCDS; CCDS48132.1; -. [Q9Y279-3]
DR   CCDS; CCDS55435.1; -. [Q9Y279-2]
DR   RefSeq; NP_001093901.1; NM_001100431.1. [Q9Y279-3]
DR   RefSeq; NP_001171759.1; NM_001184830.1. [Q9Y279-2]
DR   RefSeq; NP_001171760.1; NM_001184831.1.
DR   RefSeq; NP_001244332.1; NM_001257403.1.
DR   RefSeq; NP_009199.1; NM_007268.2. [Q9Y279-1]
DR   PDB; 2ICC; X-ray; 1.20 A; A=19-137.
DR   PDB; 2ICE; X-ray; 3.10 A; S/T=19-137.
DR   PDB; 2ICF; X-ray; 4.10 A; S=19-137.
DR   PDB; 5IMK; X-ray; 1.23 A; A=19-232.
DR   PDB; 5IML; X-ray; 1.80 A; A=19-232.
DR   PDB; 8TE5; X-ray; 1.50 A; A=20-137.
DR   PDB; 8TE6; X-ray; 1.25 A; A=20-137.
DR   PDBsum; 2ICC; -.
DR   PDBsum; 2ICE; -.
DR   PDBsum; 2ICF; -.
DR   PDBsum; 5IMK; -.
DR   PDBsum; 5IML; -.
DR   PDBsum; 8TE5; -.
DR   PDBsum; 8TE6; -.
DR   AlphaFoldDB; Q9Y279; -.
DR   SMR; Q9Y279; -.
DR   BioGRID; 116455; 207.
DR   IntAct; Q9Y279; 39.
DR   STRING; 9606.ENSP00000363869; -.
DR   GlyCosmos; Q9Y279; 1 site, 1 glycan.
DR   GlyGen; Q9Y279; 1 site, 1 O-linked glycan (1 site).
DR   iPTMnet; Q9Y279; -.
DR   PhosphoSitePlus; Q9Y279; -.
DR   SwissPalm; Q9Y279; -.
DR   BioMuta; VSIG4; -.
DR   DMDM; 59799152; -.
DR   jPOST; Q9Y279; -.
DR   MassIVE; Q9Y279; -.
DR   PaxDb; 9606-ENSP00000363869; -.
DR   PeptideAtlas; Q9Y279; -.
DR   ProteomicsDB; 85683; -. [Q9Y279-1]
DR   ProteomicsDB; 85684; -. [Q9Y279-2]
DR   ProteomicsDB; 85685; -. [Q9Y279-3]
DR   ABCD; Q9Y279; 1 sequenced antibody.
DR   Antibodypedia; 13115; 242 antibodies from 33 providers.
DR   DNASU; 11326; -.
DR   Ensembl; ENST00000374737.9; ENSP00000363869.4; ENSG00000155659.15. [Q9Y279-1]
DR   Ensembl; ENST00000412866.2; ENSP00000394143.2; ENSG00000155659.15. [Q9Y279-3]
DR   Ensembl; ENST00000455586.6; ENSP00000411581.2; ENSG00000155659.15. [Q9Y279-2]
DR   GeneID; 11326; -.
DR   KEGG; hsa:11326; -.
DR   MANE-Select; ENST00000374737.9; ENSP00000363869.4; NM_007268.3; NP_009199.1.
DR   UCSC; uc004dwh.3; human. [Q9Y279-1]
DR   AGR; HGNC:17032; -.
DR   CTD; 11326; -.
DR   DisGeNET; 11326; -.
DR   GeneCards; VSIG4; -.
DR   HGNC; HGNC:17032; VSIG4.
DR   HPA; ENSG00000155659; Tissue enhanced (lung).
DR   MIM; 300353; gene.
DR   neXtProt; NX_Q9Y279; -.
DR   OpenTargets; ENSG00000155659; -.
DR   PharmGKB; PA134986421; -.
DR   VEuPathDB; HostDB:ENSG00000155659; -.
DR   eggNOG; ENOG502S07Y; Eukaryota.
DR   GeneTree; ENSGT00390000001432; -.
DR   HOGENOM; CLU_058836_0_0_1; -.
DR   InParanoid; Q9Y279; -.
DR   OMA; DYSEDPC; -.
DR   OrthoDB; 3808804at2759; -.
DR   PhylomeDB; Q9Y279; -.
DR   TreeFam; TF336175; -.
DR   PathwayCommons; Q9Y279; -.
DR   SignaLink; Q9Y279; -.
DR   BioGRID-ORCS; 11326; 9 hits in 770 CRISPR screens.
DR   ChiTaRS; VSIG4; human.
DR   EvolutionaryTrace; Q9Y279; -.
DR   GenomeRNAi; 11326; -.
DR   Pharos; Q9Y279; Tbio.
DR   PRO; PR:Q9Y279; -.
DR   Proteomes; UP000005640; Chromosome X.
DR   RNAct; Q9Y279; Protein.
DR   Bgee; ENSG00000155659; Expressed in right lung and 178 other cell types or tissues.
DR   ExpressionAtlas; Q9Y279; baseline and differential.
DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0032991; C:protein-containing complex; IPI:UniProtKB.
DR   GO; GO:0001851; F:complement component C3b binding; IPI:UniProtKB.
DR   GO; GO:0006957; P:complement activation, alternative pathway; IEA:UniProtKB-KW.
DR   GO; GO:0045957; P:negative regulation of complement activation, alternative pathway; IPI:UniProtKB.
DR   GO; GO:0032703; P:negative regulation of interleukin-2 production; IBA:GO_Central.
DR   GO; GO:0043031; P:negative regulation of macrophage activation; IEA:InterPro.
DR   GO; GO:0042130; P:negative regulation of T cell proliferation; IBA:GO_Central.
DR   CDD; cd16082; IgC_CRIg; 1.
DR   CDD; cd16089; IgV_CRIg; 1.
DR   Gene3D; 2.60.40.10; Immunoglobulins; 2.
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; IPR003598; Ig_sub2.
DR   InterPro; IPR013106; Ig_V-set.
DR   InterPro; IPR039939; VSIG4.
DR   InterPro; IPR039944; VSIG4_IgV.
DR   PANTHER; PTHR15466; V-SET AND IMMUNOGLOBULIN DOMAIN CONTAINING 4; 1.
DR   PANTHER; PTHR15466:SF2; V-SET AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 4; 1.
DR   Pfam; PF13927; Ig_3; 1.
DR   Pfam; PF07686; V-set; 1.
DR   SMART; SM00409; IG; 2.
DR   SMART; SM00408; IGc2; 1.
DR   SMART; SM00406; IGv; 1.
DR   SUPFAM; SSF48726; Immunoglobulin; 2.
DR   PROSITE; PS50835; IG_LIKE; 2.
DR   Genevisible; Q9Y279; HS.
PE   1: Evidence at protein level;
KW   3D-structure; Alternative splicing; Complement alternate pathway;
KW   Direct protein sequencing; Disulfide bond; Immunity; Immunoglobulin domain;
KW   Innate immunity; Membrane; Reference proteome; Repeat; Signal;
KW   Transmembrane; Transmembrane helix.
FT   SIGNAL          1..19
FT                   /evidence="ECO:0000269|PubMed:15340161"
FT   CHAIN           20..399
FT                   /note="V-set and immunoglobulin domain-containing protein
FT                   4"
FT                   /id="PRO_0000015006"
FT   TOPO_DOM        20..283
FT                   /note="Extracellular"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        284..304
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TOPO_DOM        305..399
FT                   /note="Cytoplasmic"
FT                   /evidence="ECO:0000255"
FT   DOMAIN          21..131
FT                   /note="Ig-like 1"
FT   DOMAIN          143..226
FT                   /note="Ig-like 2"
FT   DISULFID        41..113
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00114,
FT                   ECO:0000269|PubMed:17051150"
FT   DISULFID        165..211
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00114"
FT   VAR_SEQ         138..232
FT                   /note="LSVSKPTVTTGSGYGFTVPQGMRISLQCQARGSPPISYIWYKQQTNNQEPIK
FT                   VATLSTLLFKPAVIADSGSYFCTAKGQVGSEQHSDIVKFVVKD -> H (in
FT                   isoform 3)"
FT                   /evidence="ECO:0000303|Ref.3"
FT                   /id="VSP_041213"
FT   VAR_SEQ         322..399
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:12975309"
FT                   /id="VSP_012813"
FT   VARIANT         108
FT                   /note="R -> W (in dbSNP:rs34581041)"
FT                   /id="VAR_049956"
FT   VARIANT         272
FT                   /note="G -> E (in dbSNP:rs34222730)"
FT                   /id="VAR_049957"
FT   VARIANT         279
FT                   /note="G -> E (in dbSNP:rs17315645)"
FT                   /id="VAR_049958"
FT   VARIANT         397
FT                   /note="S -> I (in dbSNP:rs35553694)"
FT                   /id="VAR_049959"
FT   STRAND          22..24
FT                   /evidence="ECO:0007829|PDB:5IMK"
FT   STRAND          27..32
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          37..39
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          50..58
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          60..63
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          65..71
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          74..77
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   HELIX           80..82
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   TURN            83..85
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          86..88
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          98..100
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   HELIX           105..107
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          109..118
FT                   /evidence="ECO:0007829|PDB:2ICC"
FT   STRAND          124..136
FT                   /evidence="ECO:0007829|PDB:2ICC"
SQ   SEQUENCE   399 AA;  43987 MW;  735CA3BC58185035 CRC64;
     MGILLGLLLL GHLTVDTYGR PILEVPESVT GPWKGDVNLP CTYDPLQGYT QVLVKWLVQR
     GSDPVTIFLR DSSGDHIQQA KYQGRLHVSH KVPGDVSLQL STLEMDDRSH YTCEVTWQTP
     DGNQVVRDKI TELRVQKLSV SKPTVTTGSG YGFTVPQGMR ISLQCQARGS PPISYIWYKQ
     QTNNQEPIKV ATLSTLLFKP AVIADSGSYF CTAKGQVGSE QHSDIVKFVV KDSSKLLKTK
     TEAPTTMTYP LKATSTVKQS WDWTTDMDGY LGETSAGPGK SLPVFAIILI ISLCCMVVFT
     MAYIMLCRKT SQQEHVYEAA RAHAREANDS GETMRVAIFA SGCSSDEPTS QNLGNNYSDE
     PCIGQEYQII AQINGNYARL LDTVPLDYEF LATEGKSVC
//