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Protein

Syndecan-4

Gene

SDC4

Organism
Homo sapiens (Human)
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 (PubMed:22660413).1 Publication

GO - Molecular functioni

  • thrombospondin receptor activity Source: BHF-UCL

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-HSA-1971475. A tetrasaccharide linker sequence is required for GAG synthesis.
R-HSA-2022928. HS-GAG biosynthesis.
R-HSA-2024096. HS-GAG degradation.
R-HSA-3000170. Syndecan interactions.
R-HSA-3560783. Defective B4GALT7 causes EDS, progeroid type.
R-HSA-3560801. Defective B3GAT3 causes JDSSDHD.
R-HSA-3656237. Defective EXT2 causes exostoses 2.
R-HSA-3656253. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
R-HSA-4420332. Defective B3GALT6 causes EDSP2 and SEMDJL1.
R-HSA-975634. Retinoid metabolism and transport.
SIGNORiP31431.

Protein family/group databases

TCDBi9.A.35.1.1. the peptide translocating syndecan (syndecan) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-4
Short name:
SYND4
Alternative name(s):
Amphiglycan
Ryudocan core protein
Gene namesi
Name:SDC4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:10661. SDC4.

Subcellular locationi

Isoform 1 :

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini19 – 145127ExtracellularSequence analysisAdd
BLAST
Transmembranei146 – 17025HelicalSequence analysisAdd
BLAST
Topological domaini171 – 19828CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • cell surface Source: GO_Central
  • costamere Source: Ensembl
  • extracellular exosome Source: UniProtKB
  • focal adhesion Source: Ensembl
  • Golgi lumen Source: Reactome
  • integral component of plasma membrane Source: UniProtKB
  • lysosomal lumen Source: Reactome
  • membrane raft Source: Ensembl
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35591.

Polymorphism and mutation databases

BioMutaiSDC4.
DMDMi2851418.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Sequence analysisAdd
BLAST
Chaini19 – 198180Syndecan-4PRO_0000033511Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi39 – 391O-linked (Xyl...) (heparan sulfate)By similarity
Glycosylationi61 – 611O-linked (Xyl...) (heparan sulfate)Sequence analysis
Glycosylationi63 – 631O-linked (Xyl...) (heparan sulfate)Sequence analysis

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 TIMP3.1 Publication

Keywords - PTMi

Glycoprotein, Heparan sulfate, Proteoglycan

Proteomic databases

EPDiP31431.
PaxDbiP31431.
PeptideAtlasiP31431.
PRIDEiP31431.
TopDownProteomicsiP31431-1. [P31431-1]

PTM databases

iPTMnetiP31431.
PhosphoSiteiP31431.

Miscellaneous databases

PMAP-CutDBP31431.

Expressioni

Tissue specificityi

Expressed in epithelial and fibroblastic cells.1 Publication

Gene expression databases

BgeeiENSG00000124145.
CleanExiHS_SDC4.
GenevisibleiP31431. HS.

Organism-specific databases

HPAiCAB013240.
HPA005716.

Interactioni

Subunit structurei

Homodimer. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 (By similarity). Interacts with CDCP1 and SDCBP.By similarity3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PRKCAP172522EBI-3913237,EBI-1383528
SGTAO437653EBI-3913237,EBI-347996

Protein-protein interaction databases

BioGridi112286. 14 interactions.
DIPiDIP-29945N.
IntActiP31431. 7 interactions.
MINTiMINT-140673.
STRINGi9606.ENSP00000361818.

Structurei

Secondary structure

1
198
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi192 – 1943Combined sources
Beta strandi196 – 1983Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EJPNMR-A/B171-198[»]
1EJQNMR-A/B171-198[»]
1OBYX-ray1.85P/Q193-198[»]
1YBOX-ray2.30C/D182-198[»]
ProteinModelPortaliP31431.
SMRiP31431. Positions 171-198.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31431.

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.
InParanoidiP31431.
KOiK16338.
OMAiQEPDDFE.
OrthoDBiEOG091G0OOE.
PhylomeDBiP31431.
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]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P31431-1) [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
MAPARLFALL LFFVGGVAES IRETEVIDPQ DLLEGRYFSG ALPDDEDVVG
60 70 80 90 100
PGQESDDFEL SGSGDLDDLE DSMIGPEVVH PLVPLDNHIP ERAGSGSQVP
110 120 130 140 150
TEPKKLEENE VIPKRISPVE ESEDVSNKVS MSSTVQGSNI FERTEVLAAL
160 170 180 190
IVGGIVGILF AVFLILLLMY RMKKKDEGSY DLGKKPIYKK APTNEFYA
Length:198
Mass (Da):21,642
Last modified:July 15, 1998 - v2
Checksum:i8229AA2733F77A10
GO
Isoform 2 (identifier: P31431-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     149-198: ALIVGGIVGILFAVFLILLLMYRMKKKDEGSYDLGKKPIYKKAPTNEFYA → GCPEH

Note: Soluble form, lacks the transmembrane domain.
Show »
Length:153
Mass (Da):16,545
Checksum:i25AD50751A7D2642
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti12 – 121F → L.2 Publications
Corresponds to variant rs4458268 [ dbSNP | Ensembl ].
VAR_021851

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei149 – 19850ALIVG…NEFYA → GCPEH in isoform 2. 2 PublicationsVSP_044449Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X67016 mRNA. Translation: CAA47406.1.
D13292 mRNA. Translation: BAA02550.1.
D79206 Genomic DNA. Translation: BAA19613.1.
AK312507 mRNA. Translation: BAG35408.1.
CR542045 mRNA. Translation: CAG46842.1.
CR542074 mRNA. Translation: CAG46871.1.
AK222695 mRNA. Translation: BAD96415.1.
AK223243 mRNA. Translation: BAD96963.1.
AL021578 Genomic DNA. Translation: CAA16520.1.
CH471077 Genomic DNA. Translation: EAW75861.1.
CH471077 Genomic DNA. Translation: EAW75862.1.
BC030805 mRNA. Translation: AAH30805.1.
AA151028 mRNA. No translation available.
AA258502 mRNA. No translation available.
CCDSiCCDS13350.1. [P31431-1]
PIRiJC1457.
RefSeqiNP_002990.2. NM_002999.3. [P31431-1]
UniGeneiHs.632267.

Genome annotation databases

EnsembliENST00000372733; ENSP00000361818; ENSG00000124145. [P31431-1]
GeneIDi6385.
KEGGihsa:6385.
UCSCiuc002xnu.4. human. [P31431-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X67016 mRNA. Translation: CAA47406.1.
D13292 mRNA. Translation: BAA02550.1.
D79206 Genomic DNA. Translation: BAA19613.1.
AK312507 mRNA. Translation: BAG35408.1.
CR542045 mRNA. Translation: CAG46842.1.
CR542074 mRNA. Translation: CAG46871.1.
AK222695 mRNA. Translation: BAD96415.1.
AK223243 mRNA. Translation: BAD96963.1.
AL021578 Genomic DNA. Translation: CAA16520.1.
CH471077 Genomic DNA. Translation: EAW75861.1.
CH471077 Genomic DNA. Translation: EAW75862.1.
BC030805 mRNA. Translation: AAH30805.1.
AA151028 mRNA. No translation available.
AA258502 mRNA. No translation available.
CCDSiCCDS13350.1. [P31431-1]
PIRiJC1457.
RefSeqiNP_002990.2. NM_002999.3. [P31431-1]
UniGeneiHs.632267.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EJPNMR-A/B171-198[»]
1EJQNMR-A/B171-198[»]
1OBYX-ray1.85P/Q193-198[»]
1YBOX-ray2.30C/D182-198[»]
ProteinModelPortaliP31431.
SMRiP31431. Positions 171-198.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112286. 14 interactions.
DIPiDIP-29945N.
IntActiP31431. 7 interactions.
MINTiMINT-140673.
STRINGi9606.ENSP00000361818.

Protein family/group databases

TCDBi9.A.35.1.1. the peptide translocating syndecan (syndecan) family.

PTM databases

iPTMnetiP31431.
PhosphoSiteiP31431.

Polymorphism and mutation databases

BioMutaiSDC4.
DMDMi2851418.

Proteomic databases

EPDiP31431.
PaxDbiP31431.
PeptideAtlasiP31431.
PRIDEiP31431.
TopDownProteomicsiP31431-1. [P31431-1]

Protocols and materials databases

DNASUi6385.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000372733; ENSP00000361818; ENSG00000124145. [P31431-1]
GeneIDi6385.
KEGGihsa:6385.
UCSCiuc002xnu.4. human. [P31431-1]

Organism-specific databases

CTDi6385.
GeneCardsiSDC4.
HGNCiHGNC:10661. SDC4.
HPAiCAB013240.
HPA005716.
MIMi600017. gene.
neXtProtiNX_P31431.
PharmGKBiPA35591.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IXIG. Eukaryota.
ENOG4111QSA. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000263414.
HOVERGENiHBG004501.
InParanoidiP31431.
KOiK16338.
OMAiQEPDDFE.
OrthoDBiEOG091G0OOE.
PhylomeDBiP31431.
TreeFamiTF320463.

Enzyme and pathway databases

ReactomeiR-HSA-1971475. A tetrasaccharide linker sequence is required for GAG synthesis.
R-HSA-2022928. HS-GAG biosynthesis.
R-HSA-2024096. HS-GAG degradation.
R-HSA-3000170. Syndecan interactions.
R-HSA-3560783. Defective B4GALT7 causes EDS, progeroid type.
R-HSA-3560801. Defective B3GAT3 causes JDSSDHD.
R-HSA-3656237. Defective EXT2 causes exostoses 2.
R-HSA-3656253. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
R-HSA-4420332. Defective B3GALT6 causes EDSP2 and SEMDJL1.
R-HSA-975634. Retinoid metabolism and transport.
SIGNORiP31431.

Miscellaneous databases

ChiTaRSiSDC4. human.
EvolutionaryTraceiP31431.
GeneWikiiSDC4.
GenomeRNAii6385.
PMAP-CutDBP31431.
PROiP31431.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000124145.
CleanExiHS_SDC4.
GenevisibleiP31431. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: P31431
Secondary accession number(s): O00773
, Q16833, Q53FN9, Q6FGN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 15, 1998
Last modified: September 7, 2016
This is version 172 of the entry and version 2 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, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.