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Protein

Syndecan-4

Gene

Sdc4

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

Functioni

Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP.By similarity

GO - Molecular functioni

  • fibronectin binding Source: RGD
  • protein kinase C binding Source: RGD
  • thrombospondin receptor activity Source: Ensembl

GO - Biological processi

  • cell adhesion Source: RGD
  • cell-cell signaling Source: RGD
  • cell migration Source: GO_Central
  • inner ear receptor stereocilium organization Source: Ensembl
  • neural tube closure Source: Ensembl
  • positive regulation of exosomal secretion Source: Ensembl
  • positive regulation of extracellular exosome assembly Source: Ensembl
  • positive regulation of focal adhesion assembly Source: RGD
  • positive regulation of protein kinase activity Source: RGD
  • positive regulation of stress fiber assembly Source: RGD
  • regulation of fibroblast migration Source: Ensembl
  • ureteric bud development Source: RGD
  • wound healing Source: Ensembl
Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-RNO-1971475. A tetrasaccharide linker sequence is required for GAG synthesis.
R-RNO-2022928. HS-GAG biosynthesis.
R-RNO-2024096. HS-GAG degradation.
R-RNO-3000170. Syndecan interactions.
R-RNO-975634. Retinoid metabolism and transport.

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-4
Short name:
SYND4
Alternative name(s):
Ryudocan core protein
Gene namesi
Name:Sdc4
Synonyms:Synd4
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 3

Organism-specific databases

RGDi3650. Sdc4.

Subcellular locationi

  • Membrane Sequence analysis; Single-pass type I membrane protein Sequence analysis
  • Secreted By similarity

  • Note: Shedding of the ectodomain produces a soluble form.By similarity

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini24 – 149ExtracellularSequence analysisAdd BLAST126
Transmembranei150 – 174HelicalSequence analysisAdd BLAST25
Topological domaini175 – 202CytoplasmicSequence analysisAdd BLAST28

GO - Cellular componenti

  • cell surface Source: RGD
  • costamere Source: RGD
  • extracellular exosome Source: Ensembl
  • focal adhesion Source: RGD
  • integral component of membrane Source: UniProtKB-KW
  • membrane raft Source: RGD
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000003351324 – 202Syndecan-4Add BLAST179

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi44O-linked (Xyl...) (heparan sulfate)Curated1
Glycosylationi65O-linked (Xyl...) (heparan sulfate)Sequence analysis1
Glycosylationi67O-linked (Xyl...) (heparan sulfate)Sequence analysis1

Post-translational modificationi

Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3 (By similarity).By similarity

Keywords - PTMi

Glycoprotein, Heparan sulfate, Proteoglycan

Proteomic databases

PaxDbiP34901.
PRIDEiP34901.

PTM databases

iPTMnetiP34901.
PhosphoSitePlusiP34901.

Expressioni

Gene expression databases

BgeeiENSRNOG00000014297.
GenevisibleiP34901. RN.

Interactioni

Subunit structurei

Homodimer. Interacts with CDCP1 and SDCBP. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Fn1P049372EBI-1173182,EBI-6127274
PrkcaP056963EBI-1173182,EBI-935801

GO - Molecular functioni

  • fibronectin binding Source: RGD
  • protein kinase C binding Source: RGD

Protein-protein interaction databases

BioGridi246895. 2 interactors.
IntActiP34901. 4 interactors.
MINTiMINT-140728.
STRINGi10116.ENSRNOP00000019386.

Structurei

Secondary structure

1202
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi200 – 202Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5A2PX-ray2.50E/F/G/H195-202[»]
ProteinModelPortaliP34901.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IXIG. Eukaryota.
ENOG4111QSA. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000263414.
HOVERGENiHBG004501.
InParanoidiP34901.
KOiK16338.
OMAiQEPDDFE.
OrthoDBiEOG091G0OOE.
PhylomeDBiP34901.
TreeFamiTF320463.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 1 hit.
PfamiPF01034. Syndecan. 1 hit.
[Graphical view]
SMARTiSM00294. 4.1m. 1 hit.
[Graphical view]
PROSITEiPS00964. SYNDECAN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P34901-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPVCLFAPL LLLLLGGFPV APGESIRETE VIDPQDLLEG RYFSGALPDD
60 70 80 90 100
EDAGGLEQDS DFELSGSGDL DDTEEPRTFP EVISPLVPLD NHIPENAQPG
110 120 130 140 150
IRVPSEPKEL EENEVIPKRV PSDVGDDDVS NKVSMSSTSQ GSNIFERTEV
160 170 180 190 200
LAALIVGGVV GILFAVFLIL LLVYRMKKKD EGSYDLGKKP IYKKAPTNEF

YA
Length:202
Mass (Da):21,962
Last modified:February 1, 1994 - v1
Checksum:i5D9C8B3BF4C0D58A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M81786 mRNA. Translation: AAA73167.1.
S61868 mRNA. Translation: AAB26725.1.
PIRiA42410.
RefSeqiNP_036781.1. NM_012649.2.
UniGeneiRn.2029.

Genome annotation databases

EnsembliENSRNOT00000019386; ENSRNOP00000019386; ENSRNOG00000014297.
GeneIDi24771.
KEGGirno:24771.
UCSCiRGD:3650. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M81786 mRNA. Translation: AAA73167.1.
S61868 mRNA. Translation: AAB26725.1.
PIRiA42410.
RefSeqiNP_036781.1. NM_012649.2.
UniGeneiRn.2029.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5A2PX-ray2.50E/F/G/H195-202[»]
ProteinModelPortaliP34901.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi246895. 2 interactors.
IntActiP34901. 4 interactors.
MINTiMINT-140728.
STRINGi10116.ENSRNOP00000019386.

PTM databases

iPTMnetiP34901.
PhosphoSitePlusiP34901.

Proteomic databases

PaxDbiP34901.
PRIDEiP34901.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000019386; ENSRNOP00000019386; ENSRNOG00000014297.
GeneIDi24771.
KEGGirno:24771.
UCSCiRGD:3650. rat.

Organism-specific databases

CTDi6385.
RGDi3650. Sdc4.

Phylogenomic databases

eggNOGiENOG410IXIG. Eukaryota.
ENOG4111QSA. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000263414.
HOVERGENiHBG004501.
InParanoidiP34901.
KOiK16338.
OMAiQEPDDFE.
OrthoDBiEOG091G0OOE.
PhylomeDBiP34901.
TreeFamiTF320463.

Enzyme and pathway databases

ReactomeiR-RNO-1971475. A tetrasaccharide linker sequence is required for GAG synthesis.
R-RNO-2022928. HS-GAG biosynthesis.
R-RNO-2024096. HS-GAG degradation.
R-RNO-3000170. Syndecan interactions.
R-RNO-975634. Retinoid metabolism and transport.

Miscellaneous databases

PROiP34901.

Gene expression databases

BgeeiENSRNOG00000014297.
GenevisibleiP34901. RN.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 1 hit.
PfamiPF01034. Syndecan. 1 hit.
[Graphical view]
SMARTiSM00294. 4.1m. 1 hit.
[Graphical view]
PROSITEiPS00964. SYNDECAN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSDC4_RAT
AccessioniPrimary (citable) accession number: P34901
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: November 2, 2016
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, Direct protein sequencing, 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.