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Q96RJ3

- TR13C_HUMAN

UniProt

Q96RJ3 - TR13C_HUMAN

Protein

Tumor necrosis factor receptor superfamily member 13C

Gene

TNFRSF13C

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 114 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    Functioni

    B-cell receptor specific for TNFSF13B/TALL1/BAFF/BLyS. Promotes the survival of mature B-cells and the B-cell response.2 Publications

    GO - Biological processi

    1. B cell costimulation Source: Ensembl
    2. B cell homeostasis Source: Ensembl
    3. positive regulation of B cell proliferation Source: Ensembl
    4. positive regulation of germinal center formation Source: Ensembl
    5. positive regulation of interferon-gamma biosynthetic process Source: Ensembl
    6. positive regulation of T cell proliferation Source: Ensembl
    7. T cell costimulation Source: Ensembl

    Keywords - Molecular functioni

    Receptor

    Keywords - Biological processi

    Adaptive immunity, Immunity

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Tumor necrosis factor receptor superfamily member 13C
    Alternative name(s):
    B-cell-activating factor receptor
    BAFF receptor
    Short name:
    BAFF-R
    BLyS receptor 3
    CD_antigen: CD268
    Gene namesi
    Name:TNFRSF13C
    Synonyms:BAFFR, BR3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 22

    Organism-specific databases

    HGNCiHGNC:17755. TNFRSF13C.

    Subcellular locationi

    GO - Cellular componenti

    1. external side of plasma membrane Source: Ensembl
    2. integral component of membrane Source: UniProtKB-KW

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Immunodeficiency, common variable, 4 (CVID4) [MIM:613494]: A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti65 – 728AGAGEAAL → V in CVID4; fails to bind TNFSF13B and fails to induce downstream NF-kappa-B processing. 1 Publication
    VAR_063889

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi24 – 241C → Y: Abolishes a disulfide bond and thereby changes the specificity, so that both TNFSF13B and TNFSF13 can be bound. 1 Publication
    Mutagenesisi26 – 261D → A: Strongly reduced affinity for TNFSF13B. 1 Publication
    Mutagenesisi28 – 281L → A: Strongly reduced affinity for TNFSF13B. 1 Publication
    Mutagenesisi35 – 351C → S: Abolishes a disulfide bond and thereby changes the specificity, so that both TNFSF13B and TNFSF13 can be bound. 1 Publication

    Keywords - Diseasei

    Disease mutation

    Organism-specific databases

    MIMi613494. phenotype.
    Orphaneti1572. Common variable immunodeficiency.
    PharmGKBiPA38466.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 184184Tumor necrosis factor receptor superfamily member 13CPRO_0000058933Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi19 ↔ 32
    Disulfide bondi24 ↔ 35

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRIDEiQ96RJ3.

    PTM databases

    PhosphoSiteiQ96RJ3.

    Expressioni

    Tissue specificityi

    Highly expressed in spleen and lymph node, and in resting B-cells. Detected at lower levels in activated B-cells, resting CD4+ T-cells, in thymus and peripheral blood leukocytes.

    Gene expression databases

    ArrayExpressiQ96RJ3.
    BgeeiQ96RJ3.
    CleanExiHS_TNFRSF13C.
    GenevestigatoriQ96RJ3.

    Organism-specific databases

    HPAiCAB008380.
    HPA003246.

    Interactioni

    Protein-protein interaction databases

    BioGridi125443. 5 interactions.
    STRINGi9606.ENSP00000291232.

    Structurei

    Secondary structure

    1
    184
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi23 – 264
    Turni27 – 304
    Beta strandi31 – 344
    Helixi35 – 373

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MPVNMR-A26-33[»]
    1OQEX-ray2.50K/L/M/N/O/P/Q/R16-46[»]
    1OSXNMR-A1-61[»]
    1P0TX-ray3.300/1/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z/a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p/q/r/s/t/u/v/w/x1-63[»]
    2HFGX-ray2.61R7-54[»]
    ProteinModelPortaliQ96RJ3.
    SMRiQ96RJ3. Positions 16-46.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ96RJ3.

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 7878ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini100 – 18485CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei79 – 9921Helical; Signal-anchor for type III membrane proteinSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati18 – 3518TNFR-Cys; truncatedAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni26 – 316Essential for TNFSF13B/TALL1/BAFF/BLyS binding

    Sequence similaritiesi

    Contains 1 TNFR-Cys repeat.Curated

    Keywords - Domaini

    Signal-anchor, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG43121.
    HOGENOMiHOG000132919.
    HOVERGENiHBG055867.
    InParanoidiQ96RJ3.
    KOiK05151.
    OMAiACKLFRT.
    OrthoDBiEOG7FBRM4.
    PhylomeDBiQ96RJ3.
    TreeFamiTF336877.

    Family and domain databases

    InterProiIPR022338. TNFR_13C.
    IPR015336. TNFR_13C_TALL-1-bd.
    [Graphical view]
    PfamiPF09256. BaffR-Tall_bind. 1 hit.
    [Graphical view]
    PRINTSiPR01964. TNFACTORR13C.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q96RJ3-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS    50
    PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLALV LALVLVGLVS 100
    WRRRQRRLRG ASSAEAPDGD KDAPEPLDKV IILSPGISDA TAPAWPPPGE 150
    DPGTTPPGHS VPVPATELGS TELVTTKTAG PEQQ 184
    Length:184
    Mass (Da):18,864
    Last modified:December 1, 2001 - v1
    Checksum:iF2BFB98099A27138
    GO
    Isoform 2 (identifier: Q96RJ3-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         143-143: P → PA

    Note: No experimental confirmation available.

    Show »
    Length:185
    Mass (Da):18,935
    Checksum:i2E64C16E672A6C64
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti64 – 641G → V.1 Publication
    VAR_063888
    Natural varianti65 – 728AGAGEAAL → V in CVID4; fails to bind TNFSF13B and fails to induce downstream NF-kappa-B processing. 1 Publication
    VAR_063889
    Natural varianti159 – 1591H → Y.1 Publication
    VAR_063890

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei143 – 1431P → PA in isoform 2. 1 PublicationVSP_006505

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF373846 mRNA. Translation: AAK91826.1.
    Z99716 Genomic DNA. No translation available.
    CCDSiCCDS14024.1. [Q96RJ3-1]
    RefSeqiNP_443177.1. NM_052945.3. [Q96RJ3-1]
    UniGeneiHs.344088.

    Genome annotation databases

    EnsembliENST00000291232; ENSP00000291232; ENSG00000159958. [Q96RJ3-1]
    GeneIDi115650.
    KEGGihsa:115650.
    UCSCiuc003bbl.2. human. [Q96RJ3-1]

    Polymorphism databases

    DMDMi21264093.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF373846 mRNA. Translation: AAK91826.1 .
    Z99716 Genomic DNA. No translation available.
    CCDSi CCDS14024.1. [Q96RJ3-1 ]
    RefSeqi NP_443177.1. NM_052945.3. [Q96RJ3-1 ]
    UniGenei Hs.344088.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1MPV NMR - A 26-33 [» ]
    1OQE X-ray 2.50 K/L/M/N/O/P/Q/R 16-46 [» ]
    1OSX NMR - A 1-61 [» ]
    1P0T X-ray 3.30 0/1/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z/a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p/q/r/s/t/u/v/w/x 1-63 [» ]
    2HFG X-ray 2.61 R 7-54 [» ]
    ProteinModelPortali Q96RJ3.
    SMRi Q96RJ3. Positions 16-46.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 125443. 5 interactions.
    STRINGi 9606.ENSP00000291232.

    Chemistry

    GuidetoPHARMACOLOGYi 1886.

    PTM databases

    PhosphoSitei Q96RJ3.

    Polymorphism databases

    DMDMi 21264093.

    Proteomic databases

    PRIDEi Q96RJ3.

    Protocols and materials databases

    DNASUi 115650.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000291232 ; ENSP00000291232 ; ENSG00000159958 . [Q96RJ3-1 ]
    GeneIDi 115650.
    KEGGi hsa:115650.
    UCSCi uc003bbl.2. human. [Q96RJ3-1 ]

    Organism-specific databases

    CTDi 115650.
    GeneCardsi GC22M042321.
    GeneReviewsi TNFRSF13C.
    HGNCi HGNC:17755. TNFRSF13C.
    HPAi CAB008380.
    HPA003246.
    MIMi 606269. gene.
    613494. phenotype.
    neXtProti NX_Q96RJ3.
    Orphaneti 1572. Common variable immunodeficiency.
    PharmGKBi PA38466.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG43121.
    HOGENOMi HOG000132919.
    HOVERGENi HBG055867.
    InParanoidi Q96RJ3.
    KOi K05151.
    OMAi ACKLFRT.
    OrthoDBi EOG7FBRM4.
    PhylomeDBi Q96RJ3.
    TreeFami TF336877.

    Miscellaneous databases

    EvolutionaryTracei Q96RJ3.
    GeneWikii TNFRSF13C.
    GenomeRNAii 115650.
    NextBioi 79628.
    PROi Q96RJ3.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q96RJ3.
    Bgeei Q96RJ3.
    CleanExi HS_TNFRSF13C.
    Genevestigatori Q96RJ3.

    Family and domain databases

    InterProi IPR022338. TNFR_13C.
    IPR015336. TNFR_13C_TALL-1-bd.
    [Graphical view ]
    Pfami PF09256. BaffR-Tall_bind. 1 hit.
    [Graphical view ]
    PRINTSi PR01964. TNFACTORR13C.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
      Tissue: B-cell lymphoma.
    2. "The DNA sequence of human chromosome 22."
      Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M.
      , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H.
      Nature 402:489-495(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "Identification of a novel receptor for B lymphocyte stimulator that is mutated in a mouse strain with severe B cell deficiency."
      Yan M., Brady J.R., Chan B., Lee W.P., Hsu B., Harless S.M., Cancro M.P., Grewal I.S., Dixit V.M.
      Curr. Biol. 11:1547-1552(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    4. "BAFF/BLyS receptor 3 binds the B cell survival factor BAFF ligand through a discrete surface loop and promotes processing of NF-kappaB2."
      Kayagaki N., Yan M., Seshasayee D., Wang H., Lee W., French D.M., Grewal I.S., Cochran A.G., Gordon N.C., Yin J., Starovasnik M.A., Dixit V.M.
      Immunity 17:515-524(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 26-33, FUNCTION, DISULFIDE BONDS.
    5. "BAFF/BLyS receptor 3 comprises a minimal TNF receptor-like module that encodes a highly focused ligand-binding site."
      Gordon N.C., Pan B., Hymowitz S.G., Yin J., Kelley R.F., Cochran A.G., Yan M., Dixit V.M., Fairbrother W.J., Starovasnik M.A.
      Biochemistry 42:5977-5983(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 1-61, X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 26-31 IN COMPLEX WITH TNFSF13B/TALL1/BAFF/BLYS, DISULFIDE BONDS, MUTAGENESIS OF ASP-26 AND LEU-28.
    6. "Ligand-receptor binding revealed by the TNF family member TALL-1."
      Liu Y., Hong X., Kappler J., Jiang L., Zhang R., Xu L., Pan C.-H., Martin W.E., Murphy R.C., Shu H.-B., Dai S., Zhang G.
      Nature 423:49-56(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 16-46 IN COMPLEX WITH TNFSF13B/TALL1/BAFF/BLYS, DISULFIDE BONDS, MUTAGENESIS OF CYS-24 AND CYS-35.
    7. "Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation."
      Kim H.M., Yu K.S., Lee M.E., Shin D.R., Kim Y.S., Paik S.-G., Yoo O.J., Lee H., Lee J.-O.
      Nat. Struct. Biol. 10:342-348(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF 1-63 IN COMPLEX WITH TNFSF13B/TALL1/BAFF/BLYS, DISULFIDE BONDS.
    8. "Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells."
      Lee C.V., Hymowitz S.G., Wallweber H.J., Gordon N.C., Billeci K.L., Tsai S.-P., Compaan D.M., Yin J., Gong Q., Kelley R.F., DeForge L.E., Martin F., Starovasnik M.A., Fuh G.
      Blood 108:3103-3111(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.61 ANGSTROMS) OF 7-54, INTERACTION WITH TNFSF13B/TALL1/BAFF/BLYS.
    9. "Mutational analysis of human BAFF receptor TNFRSF13C (BAFF-R) in patients with common variable immunodeficiency."
      Losi C.G., Silini A., Fiorini C., Soresina A., Meini A., Ferrari S., Notarangelo L.D., Lougaris V., Plebani A.
      J. Clin. Immunol. 25:496-502(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS VAL-64 AND TYR-159.
    10. Cited for: VARIANT CVID4 65-ALA--LEU-72 DELINS VAL, CHARACTERIZATION OF VARIANT CVID4 65-ALA--LEU-72 DELINS VAL.

    Entry informationi

    Entry nameiTR13C_HUMAN
    AccessioniPrimary (citable) accession number: Q96RJ3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 27, 2002
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 114 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human cell differentiation molecules
      CD nomenclature of surface proteins of human leucocytes and list of entries
    2. Human chromosome 22
      Human chromosome 22: entries, gene names and cross-references to MIM
    3. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    4. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    5. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    6. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    7. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3