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Protein

Syndecan-1

Gene

SDC1

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 both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).1 Publication

GO - Molecular functioni

  • glycoprotein binding Source: Ensembl
  • protein C-terminus binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

BioCyciZFISH:ENSG00000115884-MONOMER.
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.

Protein family/group databases

TCDBi9.A.35.1.2. the peptide translocating syndecan (syndecan) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-1
Short name:
SYND1
Alternative name(s):
CD_antigen: CD138
Gene namesi
Name:SDC1
Synonyms:SDC
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:10658. SDC1.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini23 – 254ExtracellularSequence analysisAdd BLAST232
Transmembranei255 – 275HelicalSequence analysisAdd BLAST21
Topological domaini276 – 310CytoplasmicSequence analysisAdd BLAST35

GO - Cellular componenti

  • cell surface Source: UniProtKB
  • cytoplasm Source: HPA
  • external side of plasma membrane Source: Ensembl
  • extracellular exosome Source: UniProtKB
  • focal adhesion Source: HPA
  • Golgi lumen Source: Reactome
  • integral component of plasma membrane Source: ProtInc
  • lysosomal lumen Source: Reactome
  • plasma membrane Source: Reactome
  • protein complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

DisGeNETi6382.
OpenTargetsiENSG00000115884.
PharmGKBiPA35588.

Polymorphism and mutation databases

BioMutaiSDC1.
DMDMi229463011.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 22Sequence analysisAdd BLAST22
ChainiPRO_000003349923 – 310Syndecan-1Add BLAST288

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi37O-linked (Xyl...) (chondroitin sulfate)By similarity1
Glycosylationi43N-linked (GlcNAc...)Sequence analysis1
Glycosylationi45O-linked (Xyl...) (heparan sulfate)By similarity1
Glycosylationi47O-linked (Xyl...) (heparan sulfate)By similarity1
Glycosylationi206O-linked (Xyl...) (chondroitin sulfate)By similarity1
Glycosylationi216O-linked (Xyl...) (chondroitin sulfate)By similarity1
Modified residuei285PhosphoserineCombined sources1

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei242 – 243CleavageBy similarity2

Keywords - PTMi

Glycoprotein, Heparan sulfate, Phosphoprotein, Proteoglycan

Proteomic databases

EPDiP18827.
MaxQBiP18827.
PaxDbiP18827.
PeptideAtlasiP18827.
PRIDEiP18827.

PTM databases

iPTMnetiP18827.
PhosphoSitePlusiP18827.
SwissPalmiP18827.

Miscellaneous databases

PMAP-CutDBP18827.

Expressioni

Gene expression databases

BgeeiENSG00000115884.
CleanExiHS_SDC1.
ExpressionAtlasiP18827. baseline and differential.
GenevisibleiP18827. HS.

Organism-specific databases

HPAiCAB002424.
HPA006185.

Interactioni

Subunit structurei

Interacts with CDCP1. Interacts (via C-terminus) with TIAM1 (via PDZ domain).2 Publications

GO - Molecular functioni

  • protein C-terminus binding Source: UniProtKB

Protein-protein interaction databases

BioGridi112284. 46 interactors.
DIPiDIP-1123N.
IntActiP18827. 7 interactors.
MINTiMINT-5004100.
STRINGi9606.ENSP00000254351.

Structurei

Secondary structure

1310
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi305 – 309Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GVCX-ray1.54B303-310[»]
4GVDX-ray1.85C/D303-310[»]
ProteinModelPortaliP18827.
SMRiP18827.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IYWX. Eukaryota.
ENOG410Y2QY. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000133092.
HOVERGENiHBG017783.
InParanoidiP18827.
KOiK06257.
OMAiPTKQEEF.
OrthoDBiEOG091G0EYV.
PhylomeDBiP18827.
TreeFamiTF320463.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR031190. Syndecan-1.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 1 hit.
PTHR10915:SF5. PTHR10915:SF5. 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.

P18827-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRRAALWLWL CALALSLQPA LPQIVATNLP PEDQDGSGDD SDNFSGSGAG
60 70 80 90 100
ALQDITLSQQ TPSTWKDTQL LTAIPTSPEP TGLEATAAST STLPAGEGPK
110 120 130 140 150
EGEAVVLPEV EPGLTAREQE ATPRPRETTQ LPTTHLASTT TATTAQEPAT
160 170 180 190 200
SHPHRDMQPG HHETSTPAGP SQADLHTPHT EDGGPSATER AAEDGASSQL
210 220 230 240 250
PAAEGSGEQD FTFETSGENT AVVAVEPDRR NQSPVDQGAT GASQGLLDRK
260 270 280 290 300
EVLGGVIAGG LVGLIFAVCL VGFMLYRMKK KDEGSYSLEE PKQANGGAYQ
310
KPTKQEEFYA
Length:310
Mass (Da):32,462
Last modified:May 5, 2009 - v3
Checksum:i8E9EF4A57F5FDBD0
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti19P → L in AAA60605 (PubMed:2324102).Curated1
Sequence conflicti259G → V in AAH08765 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05224276T → M.Corresponds to variant rs2230922dbSNPEnsembl.1
Natural variantiVAR_052243136L → Q.6 PublicationsCorresponds to variant rs10205485dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60306 mRNA. Translation: CAA42851.1.
J05392 mRNA. Translation: AAA60605.1.
AJ551176 mRNA. Translation: CAD80245.1.
AC104792 Genomic DNA. Translation: AAX93151.1.
CH471053 Genomic DNA. Translation: EAX00828.1.
CH471053 Genomic DNA. Translation: EAX00829.1.
CH471053 Genomic DNA. Translation: EAX00830.1.
CH471053 Genomic DNA. Translation: EAX00831.1.
BC008765 mRNA. Translation: AAH08765.1.
Z48199 Genomic DNA. Translation: CAA88235.1.
CCDSiCCDS1697.1.
PIRiA41776.
RefSeqiNP_001006947.1. NM_001006946.1.
NP_002988.3. NM_002997.4.
UniGeneiHs.224607.
Hs.665958.

Genome annotation databases

EnsembliENST00000254351; ENSP00000254351; ENSG00000115884.
ENST00000381150; ENSP00000370542; ENSG00000115884.
GeneIDi6382.
KEGGihsa:6382.
UCSCiuc002rdo.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60306 mRNA. Translation: CAA42851.1.
J05392 mRNA. Translation: AAA60605.1.
AJ551176 mRNA. Translation: CAD80245.1.
AC104792 Genomic DNA. Translation: AAX93151.1.
CH471053 Genomic DNA. Translation: EAX00828.1.
CH471053 Genomic DNA. Translation: EAX00829.1.
CH471053 Genomic DNA. Translation: EAX00830.1.
CH471053 Genomic DNA. Translation: EAX00831.1.
BC008765 mRNA. Translation: AAH08765.1.
Z48199 Genomic DNA. Translation: CAA88235.1.
CCDSiCCDS1697.1.
PIRiA41776.
RefSeqiNP_001006947.1. NM_001006946.1.
NP_002988.3. NM_002997.4.
UniGeneiHs.224607.
Hs.665958.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GVCX-ray1.54B303-310[»]
4GVDX-ray1.85C/D303-310[»]
ProteinModelPortaliP18827.
SMRiP18827.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112284. 46 interactors.
DIPiDIP-1123N.
IntActiP18827. 7 interactors.
MINTiMINT-5004100.
STRINGi9606.ENSP00000254351.

Protein family/group databases

TCDBi9.A.35.1.2. the peptide translocating syndecan (syndecan) family.

PTM databases

iPTMnetiP18827.
PhosphoSitePlusiP18827.
SwissPalmiP18827.

Polymorphism and mutation databases

BioMutaiSDC1.
DMDMi229463011.

Proteomic databases

EPDiP18827.
MaxQBiP18827.
PaxDbiP18827.
PeptideAtlasiP18827.
PRIDEiP18827.

Protocols and materials databases

DNASUi6382.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254351; ENSP00000254351; ENSG00000115884.
ENST00000381150; ENSP00000370542; ENSG00000115884.
GeneIDi6382.
KEGGihsa:6382.
UCSCiuc002rdo.2. human.

Organism-specific databases

CTDi6382.
DisGeNETi6382.
GeneCardsiSDC1.
H-InvDBHIX0161948.
HGNCiHGNC:10658. SDC1.
HPAiCAB002424.
HPA006185.
MIMi186355. gene.
neXtProtiNX_P18827.
OpenTargetsiENSG00000115884.
PharmGKBiPA35588.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IYWX. Eukaryota.
ENOG410Y2QY. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000133092.
HOVERGENiHBG017783.
InParanoidiP18827.
KOiK06257.
OMAiPTKQEEF.
OrthoDBiEOG091G0EYV.
PhylomeDBiP18827.
TreeFamiTF320463.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000115884-MONOMER.
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.

Miscellaneous databases

ChiTaRSiSDC1. human.
GeneWikiiSyndecan_1.
GenomeRNAii6382.
PMAP-CutDBP18827.
PROiP18827.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115884.
CleanExiHS_SDC1.
ExpressionAtlasiP18827. baseline and differential.
GenevisibleiP18827. HS.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR031190. Syndecan-1.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 1 hit.
PTHR10915:SF5. PTHR10915:SF5. 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 nameiSDC1_HUMAN
AccessioniPrimary (citable) accession number: P18827
Secondary accession number(s): D6W523
, Q53QV0, Q546D3, Q96HB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: May 5, 2009
Last modified: November 2, 2016
This is version 165 of the entry and version 3 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 cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 2
    Human chromosome 2: 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. 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.