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Q96RJ3 (TR13C_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:TNFRSF13C
Synonyms:BAFFR, BR3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length184 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

B-cell receptor specific for TNFSF13B/TALL1/BAFF/BLyS. Promotes the survival of mature B-cells and the B-cell response. Ref.3 Ref.4

Subcellular location

Membrane; Single-pass type III membrane protein Probable.

Tissue specificity

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.

Involvement in disease

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. Ref.10

Sequence similarities

Contains 1 TNFR-Cys repeat.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q96RJ3-1)

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.
Isoform 2 (identifier: Q96RJ3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     143-143: P → PA
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 184184Tumor necrosis factor receptor superfamily member 13C
PRO_0000058933

Regions

Topological domain1 – 7878Extracellular Potential
Transmembrane79 – 9921Helical; Signal-anchor for type III membrane protein; Potential
Topological domain100 – 18485Cytoplasmic Potential
Repeat18 – 3518TNFR-Cys; truncated
Region26 – 316Essential for TNFSF13B/TALL1/BAFF/BLyS binding

Amino acid modifications

Disulfide bond19 ↔ 32 Ref.4 Ref.5 Ref.6 Ref.7
Disulfide bond24 ↔ 35 Ref.4 Ref.5 Ref.6 Ref.7

Natural variations

Alternative sequence1431P → PA in isoform 2.
VSP_006505
Natural variant641G → V. Ref.9
VAR_063888
Natural variant65 – 728AGAGEAAL → V in CVID4; fails to bind TNFSF13B and fails to induce downstream NF-kappa-B processing.
VAR_063889
Natural variant1591H → Y. Ref.9
VAR_063890

Experimental info

Mutagenesis241C → Y: Abolishes a disulfide bond and thereby changes the specificity, so that both TNFSF13B and TNFSF13 can be bound. Ref.6
Mutagenesis261D → A: Strongly reduced affinity for TNFSF13B. Ref.5
Mutagenesis281L → A: Strongly reduced affinity for TNFSF13B. Ref.5
Mutagenesis351C → S: Abolishes a disulfide bond and thereby changes the specificity, so that both TNFSF13B and TNFSF13 can be bound. Ref.6

Secondary structure

...... 184
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: F2BFB98099A27138

FASTA18418,864
        10         20         30         40         50         60 
MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ 

        70         80         90        100        110        120 
ESVGAGAGEA ALPLPGLLFG APALLGLALV LALVLVGLVS WRRRQRRLRG ASSAEAPDGD 

       130        140        150        160        170        180 
KDAPEPLDKV IILSPGISDA TAPAWPPPGE DPGTTPPGHS VPVPATELGS TELVTTKTAG 


PEQQ 

« Hide

Isoform 2 [UniParc].

Checksum: 2E64C16E672A6C64
Show »

FASTA18518,935

References

« Hide 'large scale' references
[1]"BAFF-R, a newly identified TNF receptor that specifically interacts with BAFF."
Thompson J.S., Bixler S.A., Qian F., Vora K., Scott M.L., Cachero T.G., Hession C., Schneider P., Sizing I.D., Mullen C., Strauch K., Zafari M., Benjamin C.D., Tschopp J., Browning J.L., Ambrose C.
Science 293:2108-2111(2001) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]"B-cell activating factor receptor deficiency is associated with an adult-onset antibody deficiency syndrome in humans."
Warnatz K., Salzer U., Rizzi M., Fischer B., Gutenberger S., Boehm J., Kienzler A.-K., Pan-Hammarstroem Q., Hammarstroem L., Rakhmanov M., Schlesier M., Grimbacher B., Peter H.-H., Eibel H.
Proc. Natl. Acad. Sci. U.S.A. 106:13945-13950(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT CVID4 65-ALA--LEU-72 DELINS VAL, CHARACTERIZATION OF VARIANT CVID4 65-ALA--LEU-72 DELINS VAL.
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF373846 mRNA. Translation: AAK91826.1.
Z99716 Genomic DNA. No translation available.
RefSeqNP_443177.1. NM_052945.3.
UniGeneHs.344088.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ96RJ3.
SMRQ96RJ3. Positions 16-46.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid125443. 5 interactions.
STRING9606.ENSP00000291232.

Chemistry

GuidetoPHARMACOLOGY1886.

PTM databases

PhosphoSiteQ96RJ3.

Polymorphism databases

DMDM21264093.

Proteomic databases

PRIDEQ96RJ3.

Protocols and materials databases

DNASU115650.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000291232; ENSP00000291232; ENSG00000159958. [Q96RJ3-1]
GeneID115650.
KEGGhsa:115650.
UCSCuc003bbl.2. human. [Q96RJ3-1]

Organism-specific databases

CTD115650.
GeneCardsGC22M042321.
HGNCHGNC:17755. TNFRSF13C.
HPACAB008380.
HPA003246.
MIM606269. gene.
613494. phenotype.
neXtProtNX_Q96RJ3.
Orphanet1572. Common variable immunodeficiency.
PharmGKBPA38466.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG43121.
HOGENOMHOG000132919.
HOVERGENHBG055867.
InParanoidQ96RJ3.
KOK05151.
OMAACKLFRT.
OrthoDBEOG7FBRM4.
PhylomeDBQ96RJ3.
TreeFamTF336877.

Gene expression databases

ArrayExpressQ96RJ3.
BgeeQ96RJ3.
CleanExHS_TNFRSF13C.
GenevestigatorQ96RJ3.

Family and domain databases

InterProIPR022338. TNFR_13C.
IPR015336. TNFR_13C_TALL-1-bd.
[Graphical view]
PfamPF09256. BaffR-Tall_bind. 1 hit.
[Graphical view]
PRINTSPR01964. TNFACTORR13C.
ProtoNetSearch...

Other

EvolutionaryTraceQ96RJ3.
GeneWikiTNFRSF13C.
GenomeRNAi115650.
NextBio79628.
PROQ96RJ3.
SOURCESearch...

Entry information

Entry nameTR13C_HUMAN
AccessionPrimary (citable) accession number: Q96RJ3
Entry history
Integrated into UniProtKB/Swiss-Prot: May 27, 2002
Last sequence update: December 1, 2001
Last modified: April 16, 2014
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 22

Human chromosome 22: entries, gene names and cross-references to MIM

Human cell differentiation molecules

CD nomenclature of surface proteins of human leucocytes and list of entries