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Protein

Syntenin-1

Gene

Sdcbp

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Multifunctional adapter protein involved in diverse array of functions including trafficking of transmembrane proteins, neuro and immunomodulation, exosome biogenesis, and tumorigenesis. Positively regulates TGFB1-mediated SMAD2/3 activation and TGFB1-induced epithelial-to-mesenchymal transition (EMT) and cell migration in various cell types. May increase TGFB1 signaling by enhancing cell-surface expression of TGFR1 by preventing the interaction between TGFR1 and CAV1 and subsequent CAV1-dependent internalization and degradation of TGFR1. In concert with SDC1/4 and PDCD6IP, regulates exosome biogenesis. Regulates migration, growth, proliferation, and cell cycle progression in a variety of cancer types. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.By similarity

GO - Molecular functioni

  • cell adhesion molecule binding Source: RGD
  • ephrin receptor binding Source: RGD
  • glycoprotein binding Source: RGD
  • growth factor binding Source: RGD
  • interleukin-5 receptor binding Source: UniProtKB
  • neurexin family protein binding Source: UniProtKB
  • protein C-terminus binding Source: RGD
  • protein heterodimerization activity Source: RGD
  • protein homodimerization activity Source: RGD
  • syndecan binding Source: RGD

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-RNO-3928664. Ephrin signaling.
R-RNO-447043. Neurofascin interactions.
R-RNO-6798695. Neutrophil degranulation.

Names & Taxonomyi

Protein namesi
Recommended name:
Syntenin-1
Alternative name(s):
Syndecan-binding protein 1
Gene namesi
Name:Sdcbp
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi621497. Sdcbp.

Subcellular locationi

  • Cell junctionfocal adhesion By similarity
  • Cell junctionadherens junction By similarity
  • Cell membrane By similarity; Peripheral membrane protein By similarity
  • Endoplasmic reticulum membrane By similarity; Peripheral membrane protein By similarity
  • Nucleus By similarity
  • Melanosome By similarity
  • Cytoplasmcytosol By similarity
  • Cytoplasmcytoskeleton By similarity
  • Secretedexosome By similarity
  • Membrane raft By similarity

  • Note: Mainly membrane-associated. Localized to adherens junctions, focal adhesions and endoplasmic reticulum. Colocalized with actin stress fibers. Also found in the nucleus. Identified by mass spectrometry in melanosome fractions from stage I to stage IV.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Cytoplasm, Cytoskeleton, Endoplasmic reticulum, Membrane, Nucleus, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00001840032 – 300Syntenin-1Add BLAST299

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei6PhosphoserineCombined sources1
Modified residuei48PhosphotyrosineBy similarity1

Post-translational modificationi

Phosphorylated on tyrosine residues.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ9JI92.
PRIDEiQ9JI92.

PTM databases

iPTMnetiQ9JI92.
PhosphoSitePlusiQ9JI92.

Expressioni

Gene expression databases

BgeeiENSRNOG00000009683.
GenevisibleiQ9JI92. RN.

Interactioni

Subunit structurei

Monomer and homodimer. Interacts with neurofascin and SDCBP2 (PubMed:11152476). Interacts with PTPRJ (PubMed:11434923). Interacts with SDC1, SDC2, SDC3, SDC4, NRXN2, EPHA7, EPHB1, NF2 isoform 1, TGFA and IL5RA (By similarity). Interacts with PDCD6IP. Forms a complex with PDCD6IP and SDC2. Interacts (via C-terminus) with TGFBR1 (By similarity).By similarity2 Publications

GO - Molecular functioni

  • cell adhesion molecule binding Source: RGD
  • ephrin receptor binding Source: RGD
  • growth factor binding Source: RGD
  • interleukin-5 receptor binding Source: UniProtKB
  • neurexin family protein binding Source: UniProtKB
  • protein C-terminus binding Source: RGD
  • protein heterodimerization activity Source: RGD
  • protein homodimerization activity Source: RGD
  • syndecan binding Source: RGD

Protein-protein interaction databases

BioGridi249867. 8 interactors.
IntActiQ9JI92. 10 interactors.
MINTiMINT-1776939.
STRINGi10116.ENSRNOP00000013563.

Structurei

Secondary structure

1300
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi114 – 120Combined sources7
Beta strandi123 – 125Combined sources3
Beta strandi128 – 134Combined sources7
Beta strandi137 – 143Combined sources7
Beta strandi145 – 147Combined sources3
Helixi150 – 152Combined sources3
Beta strandi159 – 163Combined sources5
Helixi173 – 181Combined sources9
Beta strandi185 – 193Combined sources9
Beta strandi199 – 204Combined sources6
Beta strandi213 – 216Combined sources4
Beta strandi219 – 223Combined sources5
Helixi228 – 231Combined sources4
Beta strandi236 – 243Combined sources8
Helixi253 – 261Combined sources9
Beta strandi265 – 273Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5A2PX-ray2.50A/B/C/D112-274[»]
ProteinModelPortaliQ9JI92.
SMRiQ9JI92.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini116 – 195PDZ 1PROSITE-ProRule annotationAdd BLAST80
Domaini200 – 274PDZ 2PROSITE-ProRule annotationAdd BLAST75

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 104Interaction with PDCD6IPBy similarityAdd BLAST103

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi3 – 7LYPX(n)L motif 1By similarity5
Motifi47 – 51LYPX(n)L motif 2By similarity5
Motifi51 – 55LYPX(n)L motif 3By similarity5

Sequence similaritiesi

Contains 2 PDZ (DHR) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IEB7. Eukaryota.
ENOG410YNPQ. LUCA.
GeneTreeiENSGT00390000014465.
HOGENOMiHOG000231604.
HOVERGENiHBG053211.
InParanoidiQ9JI92.
KOiK17254.
OMAiHICEING.
OrthoDBiEOG091G0HJI.
PhylomeDBiQ9JI92.
TreeFamiTF327131.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
InterProiIPR001478. PDZ.
IPR030528. SDCBP.
[Graphical view]
PANTHERiPTHR12345:SF10. PTHR12345:SF10. 1 hit.
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9JI92-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLYPSLEDL KVDKVIQAQT ASSANPASQA FFLNVVDSAA FPPGGNLYPK
60 70 80 90 100
LYPELSQYMG LSLSEAEICE NMPVVSGAPT QGQLVARPSS VNYMVAPVTG
110 120 130 140 150
NDAGIRRAEI KQGIREVILC KDQDGKIGLR LKSVDNGIFV QLVQANSPAS
160 170 180 190 200
LVGLRFGDQV LQINGENCAG WSSDKAHKVL KQAFGEKITM TIRDRPFERT
210 220 230 240 250
VTMHKDSSGH VGFIFKSGKI TSIVKDSSAA RNGLLTDHHI CEINGQNVIG
260 270 280 290 300
LKDAQIADIL STAGTVVTIT IMPAFIFEHI IKRMAPSIMK SLMDHTIPEV
Length:300
Mass (Da):32,423
Last modified:October 1, 2000 - v1
Checksum:iF52D8918DE17F710
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF248548 mRNA. Translation: AAF86960.1.
AJ292243 mRNA. Translation: CAC21602.1.
BC064651 mRNA. Translation: AAH64651.1.
RefSeqiNP_114192.1. NM_031986.1.
UniGeneiRn.4309.

Genome annotation databases

EnsembliENSRNOT00000013563; ENSRNOP00000013563; ENSRNOG00000009683.
GeneIDi83841.
KEGGirno:83841.
UCSCiRGD:621497. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF248548 mRNA. Translation: AAF86960.1.
AJ292243 mRNA. Translation: CAC21602.1.
BC064651 mRNA. Translation: AAH64651.1.
RefSeqiNP_114192.1. NM_031986.1.
UniGeneiRn.4309.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5A2PX-ray2.50A/B/C/D112-274[»]
ProteinModelPortaliQ9JI92.
SMRiQ9JI92.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249867. 8 interactors.
IntActiQ9JI92. 10 interactors.
MINTiMINT-1776939.
STRINGi10116.ENSRNOP00000013563.

PTM databases

iPTMnetiQ9JI92.
PhosphoSitePlusiQ9JI92.

Proteomic databases

PaxDbiQ9JI92.
PRIDEiQ9JI92.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000013563; ENSRNOP00000013563; ENSRNOG00000009683.
GeneIDi83841.
KEGGirno:83841.
UCSCiRGD:621497. rat.

Organism-specific databases

CTDi6386.
RGDi621497. Sdcbp.

Phylogenomic databases

eggNOGiENOG410IEB7. Eukaryota.
ENOG410YNPQ. LUCA.
GeneTreeiENSGT00390000014465.
HOGENOMiHOG000231604.
HOVERGENiHBG053211.
InParanoidiQ9JI92.
KOiK17254.
OMAiHICEING.
OrthoDBiEOG091G0HJI.
PhylomeDBiQ9JI92.
TreeFamiTF327131.

Enzyme and pathway databases

ReactomeiR-RNO-3928664. Ephrin signaling.
R-RNO-447043. Neurofascin interactions.
R-RNO-6798695. Neutrophil degranulation.

Miscellaneous databases

PROiQ9JI92.

Gene expression databases

BgeeiENSRNOG00000009683.
GenevisibleiQ9JI92. RN.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
InterProiIPR001478. PDZ.
IPR030528. SDCBP.
[Graphical view]
PANTHERiPTHR12345:SF10. PTHR12345:SF10. 1 hit.
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSDCB1_RAT
AccessioniPrimary (citable) accession number: Q9JI92
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 108 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.