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Protein

Tumor necrosis factor receptor superfamily member 11B

Gene

Tnfrsf11b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as decoy receptor for TNFSF11/RANKL and thereby neutralizes its function in osteoclastogenesis. Inhibits the activation of osteoclasts and promotes osteoclast apoptosis in vitro. Bone homeostasis seems to depend on the local ratio between TNFSF11 and TNFRSF11B. May also play a role in preventing arterial calcification. May act as decoy receptor for TNFSF10/TRAIL and protect against apoptosis. TNFSF10/TRAIL binding blocks the inhibition of osteoclastogenesis.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei400 – 4001Involved in dimerizationBy similarity

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Apoptosis

Names & Taxonomyi

Protein namesi
Recommended name:
Tumor necrosis factor receptor superfamily member 11B
Alternative name(s):
Osteoclastogenesis inhibitory factor
Osteoprotegerin
Gene namesi
Name:Tnfrsf11b
Synonyms:Ocif, Opg
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:109587. Tnfrsf11b.

Subcellular locationi

GO - Cellular componenti

  • extracellular space Source: MGI
  • proteinaceous extracellular matrix Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2121By similarityAdd
BLAST
Chaini22 – 401380Tumor necrosis factor receptor superfamily member 11BPRO_0000034588Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi41 ↔ 54PROSITE-ProRule annotation1 Publication
Disulfide bondi44 ↔ 62PROSITE-ProRule annotation1 Publication
Disulfide bondi65 ↔ 80PROSITE-ProRule annotation1 Publication
Disulfide bondi83 ↔ 97PROSITE-ProRule annotation1 Publication
Disulfide bondi87 ↔ 105PROSITE-ProRule annotation1 Publication
Glycosylationi98 – 981N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi107 ↔ 118PROSITE-ProRule annotation1 Publication
Disulfide bondi124 ↔ 142PROSITE-ProRule annotation1 Publication
Disulfide bondi145 ↔ 160PROSITE-ProRule annotation1 Publication
Glycosylationi165 – 1651N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi166 ↔ 185PROSITE-ProRule annotation1 Publication
Glycosylationi178 – 1781N-linked (GlcNAc...)Sequence Analysis
Glycosylationi289 – 2891N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PRIDEiO08712.

PTM databases

PhosphoSiteiO08712.

Expressioni

Tissue specificityi

Highly expressed in liver, lung, stomach, intestines and calvaria. Highly expressed in decidua and placenta, and in embryo.

Developmental stagei

Detected in embryo at high levels on day 7, whereas expression decreases at day 11 and increases from day 15 to 17. On day 15 found in developing bone primordia, brachiocephalic artery and ductus arteriosus, left main bronchus, abdominal aorta and midgut.

Inductioni

Up-regulated by TGF-beta and estrogens. Down-regulated by 1,25-dihdroxyvitamin D3 and parathyroid hormone.

Gene expression databases

BgeeiO08712.
ExpressionAtlasiO08712. baseline and differential.
GenevisibleiO08712. MM.

Interactioni

Subunit structurei

Homodimer. Interacts with TNFSF10 and TNFSF11.1 Publication

Protein-protein interaction databases

DIPiDIP-59980N.
STRINGi10090.ENSMUSP00000078705.

Structurei

Secondary structure

1
401
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi35 – 373Combined sources
Beta strandi48 – 525Combined sources
Beta strandi56 – 583Combined sources
Beta strandi61 – 644Combined sources
Beta strandi91 – 955Combined sources
Beta strandi99 – 1013Combined sources
Beta strandi104 – 1074Combined sources
Beta strandi111 – 1144Combined sources
Beta strandi117 – 1204Combined sources
Beta strandi128 – 1325Combined sources
Beta strandi141 – 1444Combined sources
Beta strandi155 – 1573Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4E4DX-ray2.70R22-197[»]
ProteinModelPortaliO08712.
SMRiO08712. Positions 28-162, 280-361.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati24 – 6239TNFR-Cys 1Add
BLAST
Repeati65 – 10541TNFR-Cys 2Add
BLAST
Repeati107 – 14236TNFR-Cys 3Add
BLAST
Repeati145 – 18541TNFR-Cys 4Add
BLAST
Domaini198 – 26972Death 1PROSITE-ProRule annotationAdd
BLAST
Domaini283 – 36583Death 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 2 death domains.PROSITE-ProRule annotation
Contains 4 TNFR-Cys repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

eggNOGiNOG80702.
HOGENOMiHOG000273896.
HOVERGENiHBG061495.
InParanoidiO08712.
KOiK05148.
OMAiDIDLCEN.
OrthoDBiEOG786H2Q.
PhylomeDBiO08712.
TreeFamiTF331157.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
InterProiIPR011029. DEATH-like_dom.
IPR000488. Death_domain.
IPR001368. TNFR/NGFR_Cys_rich_reg.
IPR022323. TNFR_11.
IPR017371. TNFR_11B.
[Graphical view]
PfamiPF00531. Death. 1 hit.
PF00020. TNFR_c6. 1 hit.
[Graphical view]
PIRSFiPIRSF038065. TNFR_11B. 1 hit.
PRINTSiPR01961. TNFACTORR11.
PR01975. TNFACTORR11B.
SMARTiSM00005. DEATH. 1 hit.
SM00208. TNFR. 4 hits.
[Graphical view]
SUPFAMiSSF47986. SSF47986. 2 hits.
PROSITEiPS50017. DEATH_DOMAIN. 1 hit.
PS00652. TNFR_NGFR_1. 1 hit.
PS50050. TNFR_NGFR_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O08712-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKWLCCALL VLLDIIEWTT QETLPPKYLH YDPETGHQLL CDKCAPGTYL
60 70 80 90 100
KQHCTVRRKT LCVPCPDHSY TDSWHTSDEC VYCSPVCKEL QSVKQECNRT
110 120 130 140 150
HNRVCECEEG RYLEIEFCLK HRSCPPGSGV VQAGTPERNT VCKKCPDGFF
160 170 180 190 200
SGETSSKAPC IKHTNCSTFG LLLIQKGNAT HDNVCSGNRE ATQKCGIDVT
210 220 230 240 250
LCEEAFFRFA VPTKIIPNWL SVLVDSLPGT KVNAESVERI KRRHSSQEQT
260 270 280 290 300
FQLLKLWKHQ NRDQEMVKKI IQDIDLCESS VQRHLGHSNL TTEQLLALME
310 320 330 340 350
SLPGKKISPE EIERTRKTCK SSEQLLKLLS LWRIKNGDQD TLKGLMYALK
360 370 380 390 400
HLKTSHFPKT VTHSLRKTMR FLHSFTMYRL YQKLFLEMIG NQVQSVKISC

L
Length:401
Mass (Da):45,923
Last modified:July 1, 1997 - v1
Checksum:iCAA6102D3B312470
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti138 – 1381R → P in strain: 129/Ola and NIH Swiss. 1 Publication
Natural varianti161 – 1611I → R in strain: 129/Ola and NIH Swiss. 1 Publication
Natural varianti165 – 1651N → D in strain: 129/Ola and NIH Swiss. 1 Publication
Natural varianti288 – 2881S → A in strain: 129/Ola and NIH Swiss. 1 Publication
Natural varianti296 – 2961L → R in strain: 129/Ola and NIH Swiss. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U94331 mRNA. Translation: AAB53708.1.
AB013898 mRNA. Translation: BAA28269.1.
AB013903 Genomic DNA. Translation: BAA33388.1.
CCDSiCCDS27468.1.
RefSeqiNP_032790.3. NM_008764.3.
UniGeneiMm.15383.

Genome annotation databases

EnsembliENSMUST00000079772; ENSMUSP00000078705; ENSMUSG00000063727.
GeneIDi18383.
KEGGimmu:18383.
UCSCiuc007vrk.1. mouse.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U94331 mRNA. Translation: AAB53708.1.
AB013898 mRNA. Translation: BAA28269.1.
AB013903 Genomic DNA. Translation: BAA33388.1.
CCDSiCCDS27468.1.
RefSeqiNP_032790.3. NM_008764.3.
UniGeneiMm.15383.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4E4DX-ray2.70R22-197[»]
ProteinModelPortaliO08712.
SMRiO08712. Positions 28-162, 280-361.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59980N.
STRINGi10090.ENSMUSP00000078705.

PTM databases

PhosphoSiteiO08712.

Proteomic databases

PRIDEiO08712.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000079772; ENSMUSP00000078705; ENSMUSG00000063727.
GeneIDi18383.
KEGGimmu:18383.
UCSCiuc007vrk.1. mouse.

Organism-specific databases

CTDi4982.
MGIiMGI:109587. Tnfrsf11b.

Phylogenomic databases

eggNOGiNOG80702.
HOGENOMiHOG000273896.
HOVERGENiHBG061495.
InParanoidiO08712.
KOiK05148.
OMAiDIDLCEN.
OrthoDBiEOG786H2Q.
PhylomeDBiO08712.
TreeFamiTF331157.

Miscellaneous databases

NextBioi293972.
PROiO08712.
SOURCEiSearch...

Gene expression databases

BgeeiO08712.
ExpressionAtlasiO08712. baseline and differential.
GenevisibleiO08712. MM.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
InterProiIPR011029. DEATH-like_dom.
IPR000488. Death_domain.
IPR001368. TNFR/NGFR_Cys_rich_reg.
IPR022323. TNFR_11.
IPR017371. TNFR_11B.
[Graphical view]
PfamiPF00531. Death. 1 hit.
PF00020. TNFR_c6. 1 hit.
[Graphical view]
PIRSFiPIRSF038065. TNFR_11B. 1 hit.
PRINTSiPR01961. TNFACTORR11.
PR01975. TNFACTORR11B.
SMARTiSM00005. DEATH. 1 hit.
SM00208. TNFR. 4 hits.
[Graphical view]
SUPFAMiSSF47986. SSF47986. 2 hits.
PROSITEiPS50017. DEATH_DOMAIN. 1 hit.
PS00652. TNFR_NGFR_1. 1 hit.
PS50050. TNFR_NGFR_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/c.
    Tissue: Kidney.
  2. "Structure of the mouse osteoclastogenesis inhibitory factor (OCIF) gene and its expression in embryogenesis."
    Mizuno A., Murakami A., Nakagawa N., Yasuda H., Tsuda E., Morinaga T., Higashio K.
    Gene 215:339-343(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], VARIANTS PRO-138; ARG-161; ASP-165; ALA-288 AND ARG-296.
    Strain: 129/Ola and NIH Swiss.
    Tissue: Fibroblast.
  3. "Osteoprotegerin reverses osteoporosis by inhibiting endosteal osteoclasts and prevents vascular calcification by blocking a process resembling osteoclastogenesis."
    Min H., Morony S., Sarosi I., Dunstan C.R., Capparelli C., Scully S., Van G., Kaufman S., Kostenuik P.J., Lacey D.L., Boyle W.J., Simonet W.S.
    J. Exp. Med. 192:463-474(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "RANKL employs distinct binding modes to engage RANK and the osteoprotegerin decoy receptor."
    Nelson C.A., Warren J.T., Wang M.W., Teitelbaum S.L., Fremont D.H.
    Structure 20:1971-1982(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 22-197 IN COMPLEX WITH TNFSF11/RANKL, DISULFIDE BONDS.

Entry informationi

Entry nameiTR11B_MOUSE
AccessioniPrimary (citable) accession number: O08712
Secondary accession number(s): O70202
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 27, 2002
Last sequence update: July 1, 1997
Last modified: June 24, 2015
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.