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Q96RJ3

- TR13C_HUMAN

UniProt

Q96RJ3 - TR13C_HUMAN

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Protein

Tumor necrosis factor receptor superfamily member 13C

Gene
TNFRSF13C, BAFFR, BR3
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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
Synonyms:BAFFR, BR3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 22

Organism-specific databases

HGNCiHGNC:17755. TNFRSF13C.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 7878Extracellular Reviewed predictionAdd
BLAST
Transmembranei79 – 9921Helical; Signal-anchor for type III membrane protein; Reviewed predictionAdd
BLAST
Topological domaini100 – 18485Cytoplasmic Reviewed predictionAdd
BLAST

GO - Cellular componenti

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

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.
Note: The disease is caused by mutations affecting the gene represented in this entry.1 Publication
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.
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 ↔ 324 Publications
Disulfide bondi24 ↔ 354 Publications

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.

Miscellaneous databases

EvolutionaryTraceiQ96RJ3.

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.

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.
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. VSP_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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 113 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

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