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Protein

Tumor necrosis factor ligand superfamily member 13B

Gene

TNFSF13B

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

Functioni

Cytokine that binds to TNFRSF13B/TACI and TNFRSF17/BCMA. TNFSF13/APRIL binds to the same 2 receptors. Together, they form a 2 ligands -2 receptors pathway involved in the stimulation of B- and T-cell function and the regulation of humoral immunity. A third B-cell specific BAFF-receptor (BAFFR/BR3) promotes the survival of mature B-cells and the B-cell response.1 Publication
Isoform 2 seems to inhibit isoform 1 secretion and bioactivity.By similarity
Isoform 3: Acts as a transcription factor for its own parent gene, in association with NF-kappa-B p50 subunit, at least in autoimmune and proliferative B-cell diseases. The presence of Delta4BAFF is essential for soluble BAFF release by IFNG/IFN-gamma-stimulated monocytes and for B-cell survival. It can directly or indirectly regulate the differential expression of a large number of genes involved in the innate immune response and the regulation of apoptosis.1 Publication

GO - Molecular functioni

  • receptor binding Source: ProtInc

GO - Biological processi

  • B cell costimulation Source: Ensembl
  • B cell homeostasis Source: Ensembl
  • cell proliferation Source: ProtInc
  • immune response Source: InterPro
  • immunoglobulin secretion Source: Ensembl
  • positive regulation of B cell proliferation Source: AgBase
  • positive regulation of cell proliferation Source: ProtInc
  • positive regulation of germinal center formation Source: Ensembl
  • positive regulation of T cell proliferation Source: Ensembl
  • signal transduction Source: ProtInc
  • T cell costimulation Source: Ensembl
  • tumor necrosis factor-mediated signaling pathway Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Cytokine

Keywords - Biological processi

Immunity

Enzyme and pathway databases

BioCyciZFISH:ENSG00000102524-MONOMER.
ReactomeiR-HSA-5668541. TNFR2 non-canonical NF-kB pathway.
R-HSA-5669034. TNFs bind their physiological receptors.
R-HSA-5676594. TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway.
SIGNORiQ9Y275.

Names & Taxonomyi

Protein namesi
Recommended name:
Tumor necrosis factor ligand superfamily member 13B
Alternative name(s):
B lymphocyte stimulator
Short name:
BLyS
B-cell-activating factor
BAFF
Dendritic cell-derived TNF-like molecule
TNF- and APOL-related leukocyte expressed ligand 1
Short name:
TALL-1
CD_antigen: CD257
Cleaved into the following 2 chains:
Gene namesi
Name:TNFSF13B
Synonyms:BAFF, BLYS, TALL1, TNFSF20, ZTNF4
ORF Names:UNQ401/PRO738
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:11929. TNFSF13B.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 46CytoplasmicSequence analysisAdd BLAST46
Transmembranei47 – 67Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST21
Topological domaini68 – 285ExtracellularSequence analysisAdd BLAST218

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • extracellular region Source: Reactome
  • extracellular space Source: UniProtKB-KW
  • integral component of membrane Source: UniProtKB
  • perinuclear region of cytoplasm Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

DisGeNETi10673.
OpenTargetsiENSG00000102524.
PharmGKBiPA434.

Chemistry databases

ChEMBLiCHEMBL2364158.
DrugBankiDB08879. Belimumab.

Polymorphism and mutation databases

BioMutaiTNFSF13B.
DMDMi13124573.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000345281 – 285Tumor necrosis factor ligand superfamily member 13b, membrane formAdd BLAST285
ChainiPRO_0000034529134 – 285Tumor necrosis factor ligand superfamily member 13b, soluble formAdd BLAST152

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi124N-linked (GlcNAc...)1
Disulfide bondi232 ↔ 245
Glycosylationi242N-linked (GlcNAc...) (high mannose)1

Post-translational modificationi

The soluble form derives from the membrane form by proteolytic processing.
Isoform 2 is not efficiently shed from the membrane unlike isoform 1.By similarity
N-glycosylated.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei133 – 134Cleavage2

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ9Y275.
PaxDbiQ9Y275.
PeptideAtlasiQ9Y275.
PRIDEiQ9Y275.

PTM databases

iPTMnetiQ9Y275.
PhosphoSitePlusiQ9Y275.

Expressioni

Tissue specificityi

Abundantly expressed in peripheral blood Leukocytes and is specifically expressed in monocytes and macrophages. Also found in the spleen, lymph node, bone marrow, T-cells and dendritic cells. A lower expression seen in placenta, heart, lung, fetal liver, thymus, and pancreas. Isoform 2 is expressed in many myeloid cell lines.1 Publication

Inductioni

Up-regulated by exposure to IFNG/IFN-gamma. Down-regulated by phorbol myristate acetate/ionomycin treatment.

Gene expression databases

BgeeiENSG00000102524.
CleanExiHS_TNFSF13B.
ExpressionAtlasiQ9Y275. baseline and differential.
GenevisibleiQ9Y275. HS.

Organism-specific databases

HPAiCAB009188.

Interactioni

Subunit structurei

Homotrimer. Isoform 2 heteromultimerizes with isoform 1, probably limiting the amount of functional isoform 1 on the cell surface. Isoform 3 is unlikely form trimers or bind to BAFF receptors.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
TNFRSF13BO148367EBI-519169,EBI-519160

GO - Molecular functioni

  • receptor binding Source: ProtInc

Protein-protein interaction databases

BioGridi115915. 51 interactors.
DIPiDIP-6225N.
IntActiQ9Y275. 2 interactors.
STRINGi9606.ENSP00000365048.

Structurei

Secondary structure

1285
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi146 – 151Combined sources6
Beta strandi158 – 160Combined sources3
Beta strandi163 – 165Combined sources3
Beta strandi168 – 181Combined sources14
Beta strandi184 – 187Combined sources4
Beta strandi191 – 201Combined sources11
Beta strandi205 – 215Combined sources11
Turni219 – 222Combined sources4
Beta strandi225 – 235Combined sources11
Beta strandi238 – 240Combined sources3
Beta strandi243 – 253Combined sources11
Beta strandi258 – 265Combined sources8
Turni274 – 276Combined sources3
Beta strandi277 – 283Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JH5X-ray3.00A/B/C/D/E/F/G/H/I/J142-285[»]
1KD7X-ray2.80A/B/C/K/L/M133-285[»]
1KXGX-ray2.00A/B/C/D/E/F134-285[»]
1OQDX-ray2.60A/B/C/D/E/F/G/H/I/J142-285[»]
1OQEX-ray2.50A/B/C/D/E/F/G/H/I/J142-285[»]
1OSGX-ray3.00A/B/C/D/E/F82-285[»]
3V56X-ray3.00A/B/C/D/E/F82-285[»]
4V46X-ray3.30A0/A1/A2/A3/A4/A5/A6/A7/A8/A9/AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ/Aa/Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar/As/At/Au/Av/Aw/Ax138-285[»]
4ZCHX-ray2.43A/B140-285[»]
ProteinModelPortaliQ9Y275.
SMRiQ9Y275.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y275.

Family & Domainsi

Sequence similaritiesi

Belongs to the tumor necrosis factor family.Curated

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IHQ4. Eukaryota.
ENOG4111XFQ. LUCA.
GeneTreeiENSGT00530000063837.
HOGENOMiHOG000036810.
HOVERGENiHBG061472.
InParanoidiQ9Y275.
KOiK05476.
OMAiYAMGHLI.
OrthoDBiEOG091G0GBQ.
PhylomeDBiQ9Y275.
TreeFamiTF332331.

Family and domain databases

Gene3Di2.60.120.40. 1 hit.
InterProiIPR006052. TNF_dom.
IPR008983. Tumour_necrosis_fac-like_dom.
[Graphical view]
PfamiPF00229. TNF. 1 hit.
[Graphical view]
SUPFAMiSSF49842. SSF49842. 1 hit.
PROSITEiPS50049. TNF_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y275-1) [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

        10         20         30         40         50
MDDSTEREQS RLTSCLKKRE EMKLKECVSI LPRKESPSVR SSKDGKLLAA
60 70 80 90 100
TLLLALLSCC LTVVSFYQVA ALQGDLASLR AELQGHHAEK LPAGAGAPKA
110 120 130 140 150
GLEEAPAVTA GLKIFEPPAP GEGNSSQNSR NKRAVQGPEE TVTQDCLQLI
160 170 180 190 200
ADSETPTIQK GSYTFVPWLL SFKRGSALEE KENKILVKET GYFFIYGQVL
210 220 230 240 250
YTDKTYAMGH LIQRKKVHVF GDELSLVTLF RCIQNMPETL PNNSCYSAGI
260 270 280
AKLEEGDELQ LAIPRENAQI SLDGDVTFFG ALKLL
Length:285
Mass (Da):31,223
Last modified:November 1, 1999 - v1
Checksum:i48ED0D7AB38C8867
GO
Isoform 2 (identifier: Q9Y275-2) [UniParc]FASTAAdd to basket
Also known as: DeltaBAFF

The sequence of this isoform differs from the canonical sequence as follows:
     142-160: Missing.

Show »
Length:266
Mass (Da):29,137
Checksum:i6BD06F90061152C6
GO
Isoform 3 (identifier: Q9Y275-3) [UniParc]FASTAAdd to basket
Also known as: Delta4BAFF

The sequence of this isoform differs from the canonical sequence as follows:
     162-164: SYT → FIY
     165-285: Missing.

Show »
Length:164
Mass (Da):17,578
Checksum:iF74F5E404973B730
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_013483105A → T.1 PublicationCorresponds to variant rs201543678dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_041183142 – 160Missing in isoform 2. 1 PublicationAdd BLAST19
Alternative sequenceiVSP_047591162 – 164SYT → FIY in isoform 3. 1 Publication3
Alternative sequenceiVSP_047592165 – 285Missing in isoform 3. 1 PublicationAdd BLAST121

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF136293 mRNA. Translation: AAD29421.1.
AF116456 mRNA. Translation: AAD25356.1.
AF132600 mRNA. Translation: AAD21092.1.
AY302751 mRNA. Translation: AAP83164.1.
HM636064 mRNA. Translation: ADK91575.1.
AF186114 mRNA. Translation: AAF01432.1.
AF134715 mRNA. Translation: AAF60219.1.
AY129225 mRNA. Translation: AAN08421.1.
EF064706 Genomic DNA. Translation: ABK41889.1.
AY358881 mRNA. Translation: AAQ89240.1.
CR541818 mRNA. Translation: CAG46617.1.
AL157762 Genomic DNA. Translation: CAH70631.1.
CH471085 Genomic DNA. Translation: EAX09099.1.
BC020674 mRNA. Translation: AAH20674.1.
AB073225 Genomic DNA. Translation: BAB90856.1.
CCDSiCCDS45067.1. [Q9Y275-2]
CCDS9509.1. [Q9Y275-1]
RefSeqiNP_001139117.1. NM_001145645.2. [Q9Y275-2]
NP_006564.1. NM_006573.4. [Q9Y275-1]
UniGeneiHs.525157.

Genome annotation databases

EnsembliENST00000375887; ENSP00000365048; ENSG00000102524. [Q9Y275-1]
ENST00000430559; ENSP00000389540; ENSG00000102524. [Q9Y275-2]
ENST00000542136; ENSP00000445334; ENSG00000102524. [Q9Y275-3]
GeneIDi10673.
KEGGihsa:10673.
UCSCiuc001vqr.4. human. [Q9Y275-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Protein Spotlight

Proteic grace - Issue 77 of December 2006

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF136293 mRNA. Translation: AAD29421.1.
AF116456 mRNA. Translation: AAD25356.1.
AF132600 mRNA. Translation: AAD21092.1.
AY302751 mRNA. Translation: AAP83164.1.
HM636064 mRNA. Translation: ADK91575.1.
AF186114 mRNA. Translation: AAF01432.1.
AF134715 mRNA. Translation: AAF60219.1.
AY129225 mRNA. Translation: AAN08421.1.
EF064706 Genomic DNA. Translation: ABK41889.1.
AY358881 mRNA. Translation: AAQ89240.1.
CR541818 mRNA. Translation: CAG46617.1.
AL157762 Genomic DNA. Translation: CAH70631.1.
CH471085 Genomic DNA. Translation: EAX09099.1.
BC020674 mRNA. Translation: AAH20674.1.
AB073225 Genomic DNA. Translation: BAB90856.1.
CCDSiCCDS45067.1. [Q9Y275-2]
CCDS9509.1. [Q9Y275-1]
RefSeqiNP_001139117.1. NM_001145645.2. [Q9Y275-2]
NP_006564.1. NM_006573.4. [Q9Y275-1]
UniGeneiHs.525157.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JH5X-ray3.00A/B/C/D/E/F/G/H/I/J142-285[»]
1KD7X-ray2.80A/B/C/K/L/M133-285[»]
1KXGX-ray2.00A/B/C/D/E/F134-285[»]
1OQDX-ray2.60A/B/C/D/E/F/G/H/I/J142-285[»]
1OQEX-ray2.50A/B/C/D/E/F/G/H/I/J142-285[»]
1OSGX-ray3.00A/B/C/D/E/F82-285[»]
3V56X-ray3.00A/B/C/D/E/F82-285[»]
4V46X-ray3.30A0/A1/A2/A3/A4/A5/A6/A7/A8/A9/AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ/Aa/Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar/As/At/Au/Av/Aw/Ax138-285[»]
4ZCHX-ray2.43A/B140-285[»]
ProteinModelPortaliQ9Y275.
SMRiQ9Y275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115915. 51 interactors.
DIPiDIP-6225N.
IntActiQ9Y275. 2 interactors.
STRINGi9606.ENSP00000365048.

Chemistry databases

ChEMBLiCHEMBL2364158.
DrugBankiDB08879. Belimumab.

PTM databases

iPTMnetiQ9Y275.
PhosphoSitePlusiQ9Y275.

Polymorphism and mutation databases

BioMutaiTNFSF13B.
DMDMi13124573.

Proteomic databases

EPDiQ9Y275.
PaxDbiQ9Y275.
PeptideAtlasiQ9Y275.
PRIDEiQ9Y275.

Protocols and materials databases

DNASUi10673.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000375887; ENSP00000365048; ENSG00000102524. [Q9Y275-1]
ENST00000430559; ENSP00000389540; ENSG00000102524. [Q9Y275-2]
ENST00000542136; ENSP00000445334; ENSG00000102524. [Q9Y275-3]
GeneIDi10673.
KEGGihsa:10673.
UCSCiuc001vqr.4. human. [Q9Y275-1]

Organism-specific databases

CTDi10673.
DisGeNETi10673.
GeneCardsiTNFSF13B.
HGNCiHGNC:11929. TNFSF13B.
HPAiCAB009188.
MIMi603969. gene.
neXtProtiNX_Q9Y275.
OpenTargetsiENSG00000102524.
PharmGKBiPA434.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IHQ4. Eukaryota.
ENOG4111XFQ. LUCA.
GeneTreeiENSGT00530000063837.
HOGENOMiHOG000036810.
HOVERGENiHBG061472.
InParanoidiQ9Y275.
KOiK05476.
OMAiYAMGHLI.
OrthoDBiEOG091G0GBQ.
PhylomeDBiQ9Y275.
TreeFamiTF332331.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000102524-MONOMER.
ReactomeiR-HSA-5668541. TNFR2 non-canonical NF-kB pathway.
R-HSA-5669034. TNFs bind their physiological receptors.
R-HSA-5676594. TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway.
SIGNORiQ9Y275.

Miscellaneous databases

EvolutionaryTraceiQ9Y275.
GeneWikiiB-cell_activating_factor.
GenomeRNAii10673.
PROiQ9Y275.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000102524.
CleanExiHS_TNFSF13B.
ExpressionAtlasiQ9Y275. baseline and differential.
GenevisibleiQ9Y275. HS.

Family and domain databases

Gene3Di2.60.120.40. 1 hit.
InterProiIPR006052. TNF_dom.
IPR008983. Tumour_necrosis_fac-like_dom.
[Graphical view]
PfamiPF00229. TNF. 1 hit.
[Graphical view]
SUPFAMiSSF49842. SSF49842. 1 hit.
PROSITEiPS50049. TNF_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTN13B_HUMAN
AccessioniPrimary (citable) accession number: Q9Y275
Secondary accession number(s): E0ADT7, Q6FHD6, Q7Z5J2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 175 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, Direct protein sequencing, Reference proteome

Documents

  1. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 13
    Human chromosome 13: 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. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  8. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.