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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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei242 – 2432CleavageBy similarity

GO - Molecular functioni

  • protein C-terminus binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_120752. HS-GAG degradation.
REACT_121248. HS-GAG biosynthesis.
REACT_121408. A tetrasaccharide linker sequence is required for GAG synthesis.
REACT_163942. Syndecan interactions.
REACT_24968. Retinoid metabolism and transport.
REACT_267741. Defective EXT2 causes exostoses 2.
REACT_267942. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
REACT_268678. Defective B3GAT3 causes JDSSDHD.
REACT_268749. Defective B4GALT7 causes EDS, progeroid type.
REACT_6841. Chylomicron-mediated lipid transport.

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
ProteomesiUP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:10658. SDC1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini23 – 254232ExtracellularSequence AnalysisAdd
BLAST
Transmembranei255 – 27521HelicalSequence AnalysisAdd
BLAST
Topological domaini276 – 31035CytoplasmicSequence AnalysisAdd
BLAST

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

PharmGKBiPA35588.

Polymorphism and mutation databases

BioMutaiSDC1.
DMDMi229463011.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2222Sequence AnalysisAdd
BLAST
Chaini23 – 310288Syndecan-1PRO_0000033499Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi37 – 371O-linked (Xyl...) (chondroitin sulfate)By similarity
Glycosylationi43 – 431N-linked (GlcNAc...)Sequence Analysis
Glycosylationi45 – 451O-linked (Xyl...) (heparan sulfate)By similarity
Glycosylationi47 – 471O-linked (Xyl...) (heparan sulfate)By similarity
Glycosylationi206 – 2061O-linked (Xyl...) (chondroitin sulfate)By similarity
Glycosylationi216 – 2161O-linked (Xyl...) (chondroitin sulfate)By similarity

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.

Keywords - PTMi

Glycoprotein, Heparan sulfate, Proteoglycan

Proteomic databases

MaxQBiP18827.
PaxDbiP18827.
PRIDEiP18827.

PTM databases

PhosphoSiteiP18827.

Miscellaneous databases

PMAP-CutDBP18827.

Expressioni

Gene expression databases

BgeeiP18827.
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

Protein-protein interaction databases

BioGridi112284. 15 interactions.
DIPiDIP-1123N.
IntActiP18827. 5 interactions.
MINTiMINT-5004100.
STRINGi9606.ENSP00000254351.

Structurei

Secondary structure

1
310
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi305 – 3095Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GVCX-ray1.54B303-310[»]
4GVDX-ray1.85C/D303-310[»]
ProteinModelPortaliP18827.
SMRiP18827. Positions 277-310.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG86393.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000133092.
HOVERGENiHBG017783.
InParanoidiP18827.
KOiK06257.
OMAiPTKQEEF.
OrthoDBiEOG79KPG2.
PhylomeDBiP18827.
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191P → L in AAA60605 (PubMed:2324102).Curated
Sequence conflicti259 – 2591G → V in AAH08765 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti76 – 761T → M.
Corresponds to variant rs2230922 [ dbSNP | Ensembl ].
VAR_052242
Natural varianti136 – 1361L → Q.6 Publications
Corresponds to variant rs10205485 [ dbSNP | Ensembl ].
VAR_052243

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.1. 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
EntryMethodResolution (Å)ChainPositionsPDBsum
4GVCX-ray1.54B303-310[»]
4GVDX-ray1.85C/D303-310[»]
ProteinModelPortaliP18827.
SMRiP18827. Positions 277-310.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112284. 15 interactions.
DIPiDIP-1123N.
IntActiP18827. 5 interactions.
MINTiMINT-5004100.
STRINGi9606.ENSP00000254351.

PTM databases

PhosphoSiteiP18827.

Polymorphism and mutation databases

BioMutaiSDC1.
DMDMi229463011.

Proteomic databases

MaxQBiP18827.
PaxDbiP18827.
PRIDEiP18827.

Protocols and materials databases

DNASUi6382.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254351; ENSP00000254351; ENSG00000115884.
ENST00000381150; ENSP00000370542; ENSG00000115884.
GeneIDi6382.
KEGGihsa:6382.
UCSCiuc002rdo.1. human.

Organism-specific databases

CTDi6382.
GeneCardsiGC02M020400.
H-InvDBHIX0161948.
HGNCiHGNC:10658. SDC1.
HPAiCAB002424.
HPA006185.
MIMi186355. gene.
neXtProtiNX_P18827.
PharmGKBiPA35588.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG86393.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000133092.
HOVERGENiHBG017783.
InParanoidiP18827.
KOiK06257.
OMAiPTKQEEF.
OrthoDBiEOG79KPG2.
PhylomeDBiP18827.
TreeFamiTF320463.

Enzyme and pathway databases

ReactomeiREACT_120752. HS-GAG degradation.
REACT_121248. HS-GAG biosynthesis.
REACT_121408. A tetrasaccharide linker sequence is required for GAG synthesis.
REACT_163942. Syndecan interactions.
REACT_24968. Retinoid metabolism and transport.
REACT_267741. Defective EXT2 causes exostoses 2.
REACT_267942. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
REACT_268678. Defective B3GAT3 causes JDSSDHD.
REACT_268749. Defective B4GALT7 causes EDS, progeroid type.
REACT_6841. Chylomicron-mediated lipid transport.

Miscellaneous databases

ChiTaRSiSDC1. human.
GeneWikiiSyndecan_1.
GenomeRNAii6382.
NextBioi24782.
PMAP-CutDBP18827.
PROiP18827.
SOURCEiSearch...

Gene expression databases

BgeeiP18827.
CleanExiHS_SDC1.
ExpressionAtlasiP18827. baseline and differential.
GenevisibleiP18827. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Differential expression of cell surface heparan sulfate proteoglycans in human mammary epithelial cells and lung fibroblasts."
    Lories V., Cassiman J.-J., van de Berghe H., David G.
    J. Biol. Chem. 267:1116-1122(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-136.
    Tissue: Fibroblast.
  2. "Sequence of human syndecan indicates a novel gene family of integral membrane proteoglycans."
    Mali M., Jaakkola P., Arvilommi A.-M., Jalkanen M.
    J. Biol. Chem. 265:6884-6889(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-136.
    Tissue: Mammary gland.
  3. "Shift of syndecan-1 expression from epithelial to stromal cells during progression of solid tumours."
    Mennerich D., Vogel A., Klaman I., Dahl E., Lichtner R.B., Rosenthal A., Pohlenz H.D., Thierauch K.H., Sommer A.
    Eur. J. Cancer 40:1373-1382(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-136.
  4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLN-136.
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-136.
    Tissue: Kidney.
  7. "The mapping and visual ordering of the human syndecan-1 and N-myc genes near the telomeric region of chromosome 2p."
    Kaukonen J., Alanen-Kurki L., Jalkanen M., Palotie A.
    Hum. Genet. 99:295-297(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 23-310, VARIANT GLN-136.
    Tissue: Placenta.
  8. "Regulated shedding of syndecan-1 and -4 ectodomains by thrombin and growth factor receptor activation."
    Subramanian S.V., Fitzgerald M.L., Bernfield M.
    J. Biol. Chem. 272:14713-14720(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: SHEDDING.
  9. "Adhesion signaling by a novel mitotic substrate of src kinases."
    Bhatt A.S., Erdjument-Bromage H., Tempst P., Craik C.S., Moasser M.M.
    Oncogene 24:5333-5343(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CDCP1.
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  12. "The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics."
    Liu X., Shepherd T.R., Murray A.M., Xu Z., Fuentes E.J.
    Structure 21:342-354(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) OF 303-310 IN COMPLEX WITH TIAM1, INTERACTION WITH TIAM1.

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: June 24, 2015
This is version 151 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

External Data

Dasty 3

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 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.