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Protein

Syndecan-1

Gene

SDC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

  • identical protein binding Source: IntAct
  • protein C-terminus binding Source: UniProtKB

GO - Biological processi

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-202733 Cell surface interactions at the vascular wall
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-449836 Other interleukin signaling
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

EuPathDBiHostDB:ENSG00000115884.10
HGNCiHGNC:10658 SDC1
MIMi186355 gene
neXtProtiNX_P18827

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

Keywords - Cellular componenti

Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

DisGeNETi6382
OpenTargetsiENSG00000115884
PharmGKBiPA35588

Chemistry databases

ChEMBLiCHEMBL3712898

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) serineBy similarity1
Glycosylationi43N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi45O-linked (Xyl...) (heparan sulfate) serineBy similarity1
Glycosylationi47O-linked (Xyl...) (heparan sulfate) serineBy similarity1
Glycosylationi206O-linked (Xyl...) (chondroitin sulfate) serineBy similarity1
Glycosylationi216O-linked (Xyl...) (chondroitin sulfate) serineBy 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
ProteomicsDBi53609

PTM databases

iPTMnetiP18827
PhosphoSitePlusiP18827
SwissPalmiP18827

Miscellaneous databases

PMAP-CutDBiP18827

Expressioni

Gene expression databases

BgeeiENSG00000115884 Expressed in 175 organ(s), highest expression level in vagina
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

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi112284, 54 interactors
ComplexPortaliCPX-3282 Syndecan-1-syntenin-1-ALIX complex
DIPiDIP-1123N
ELMiP18827
IntActiP18827, 11 interactors
STRINGi9606.ENSP00000254351

Structurei

Secondary structure

1310
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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
OMAiGEQDFTF
OrthoDBiEOG091G0EYV
PhylomeDBiP18827
TreeFamiTF320463

Family and domain databases

InterProiView protein in InterPro
IPR003585 Neurexin-like
IPR001050 Syndecan
IPR031190 Syndecan-1
IPR027789 Syndecan/Neurexin_dom
IPR030479 Syndecan_CS
PANTHERiPTHR10915 PTHR10915, 1 hit
PTHR10915:SF5 PTHR10915:SF5, 1 hit
PfamiView protein in Pfam
PF01034 Syndecan, 1 hit
SMARTiView protein in SMART
SM00294 4.1m, 1 hit
PROSITEiView protein in PROSITE
PS00964 SYNDECAN, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 3 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E9PHH3E9PHH3_HUMAN
Syndecan-1
SDC1
169Annotation score:
H7C1K4H7C1K4_HUMAN
Syndecan-1
SDC1
215Annotation score:
F8WCX9F8WCX9_HUMAN
Syndecan-1
SDC1
28Annotation score:

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 dbSNP:rs2230922Ensembl.1
Natural variantiVAR_052243136L → Q6 PublicationsCorresponds to variant dbSNP:rs10205485Ensembl.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

Similar proteinsi

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[»]
6EJEX-ray2.43B201-212[»]
ProteinModelPortaliP18827
SMRiP18827
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112284, 54 interactors
ComplexPortaliCPX-3282 Syndecan-1-syntenin-1-ALIX complex
DIPiDIP-1123N
ELMiP18827
IntActiP18827, 11 interactors
STRINGi9606.ENSP00000254351

Chemistry databases

ChEMBLiCHEMBL3712898

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
ProteomicsDBi53609

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
EuPathDBiHostDB:ENSG00000115884.10
GeneCardsiSDC1
H-InvDBiHIX0161948
HGNCiHGNC:10658 SDC1
HPAiCAB002424
HPA006185
MIMi186355 gene
neXtProtiNX_P18827
OpenTargetsiENSG00000115884
PharmGKBiPA35588
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IYWX Eukaryota
ENOG410Y2QY LUCA
GeneTreeiENSGT00530000063116
HOGENOMiHOG000133092
HOVERGENiHBG017783
InParanoidiP18827
KOiK06257
OMAiGEQDFTF
OrthoDBiEOG091G0EYV
PhylomeDBiP18827
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-202733 Cell surface interactions at the vascular wall
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-449836 Other interleukin signaling
R-HSA-975634 Retinoid metabolism and transport

Miscellaneous databases

ChiTaRSiSDC1 human
GeneWikiiSyndecan_1
GenomeRNAii6382
PMAP-CutDBiP18827
PROiPR:P18827
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115884 Expressed in 175 organ(s), highest expression level in vagina
CleanExiHS_SDC1
ExpressionAtlasiP18827 baseline and differential
GenevisibleiP18827 HS

Family and domain databases

InterProiView protein in InterPro
IPR003585 Neurexin-like
IPR001050 Syndecan
IPR031190 Syndecan-1
IPR027789 Syndecan/Neurexin_dom
IPR030479 Syndecan_CS
PANTHERiPTHR10915 PTHR10915, 1 hit
PTHR10915:SF5 PTHR10915:SF5, 1 hit
PfamiView protein in Pfam
PF01034 Syndecan, 1 hit
SMARTiView protein in SMART
SM00294 4.1m, 1 hit
PROSITEiView protein in PROSITE
PS00964 SYNDECAN, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSDC1_HUMAN
AccessioniPrimary (citable) accession number: P18827
Secondary accession number(s): D6W523
, Q53QV0, Q546D3, Q96HB7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: May 5, 2009
Last modified: November 7, 2018
This is version 179 of the entry and version 3 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  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. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
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