Reviewed,
UniProtKB/Swiss-Prot P48061 (SDF1_HUMAN)
Last modified
July 22, 2008.
Version 91.
History...
Clusters with 100%,
90%,
50% identity |
Documents (4) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Stromal cell-derived factor 1 Short name=SDF-1 Alternative name(s): C-X-C motif chemokine 12 Pre-B cell growth-stimulating factor Short name=PBSF Short name=hIRH Cleaved into the following 2 chains: 1- Recommended name: SDF-1-beta(3-72) 2- Recommended name: SDF-1-alpha(3-67) | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 93 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is further processed into a mature form. |
| Protein existence | Evidence at protein level. |
General annotation (Comments)
| Function | Chemoattractant active on T-lymphocytes, monocytes, but not neutrophils. SDF-1-beta(3-72) and SDF-1-alpha(3-67) show a reduced chemotactic activity. Binding to cell surface proteoglycans seems to inhibit formation of SDF-1-alpha(3-67) and thus to preserve activity on local sites. |
| Subcellular location | |
| Post-translational modification | Processed forms SDF-1-beta(3-72) and SDF-1-alpha(3-67) are produced after secretion by proteolytic cleavage of isoforms Beta and Alpha, respectively. The N-terminal processing is probably achieved by DPP4. Isoform Alpha is first cleaved at the C-terminus to yield a SDF-1-alpha(1-67) intermediate before being processsed at the N-terminus. The C-terminal processing of isoform Alpha is reduced by binding to heparin and, probably, cell surface proteoglycans. |
| Sequence similarities | Belongs to the intercrine alpha (chemokine CxC) family. |
Ontologies
Keywords | |
|---|---|
| Biological process | Chemotaxis |
| Cellular component | Secreted |
| Coding sequence diversity | Alternative splicing |
| Domain | Signal |
| Molecular function | Cytokine Growth factor |
| Technical term | 3D-structure |
Gene Ontology (GO) | |
| Biological process | G-protein coupled receptor protein signaling pathway Traceable author statement. Source: ProtInc blood circulationTraceable author statement. Source: ProtInc cell adhesionTraceable author statement. Source: ProtInc cellular calcium ion homeostasisTraceable author statement. Source: ProtInc chemotaxisTraceable author statement. Source: ProtInc immune responseTraceable author statement. Source: ProtInc regulation of actin polymerization and/or depolymerizationTraceable author statement. Source: ProtInc response to virusTraceable author statement. Source: ProtInc |
| Molecular function | chemokine activity Traceable author statement. Source: ProtInc signal transducer activityTraceable author statement. Source: ProtInc |
| Complete GO annotation... | |
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] | |||||
| Isoform Beta (identifier: P48061-1) Also known as: SDF-1-beta(1-72); 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. | |||||
| Isoform Alpha (identifier: P48061-2) Also known as: SDF-1-alpha(1-68); The sequence of this isoform differs from the canonical sequence as follows: 90-93: Missing. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | ||||||||||||||||
Molecule processing | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Signal peptide | 1 – 21 | 21 | Potential | |||||||||||||||||
| Chain | 22 – 93 | 72 | Stromal cell-derived factor 1 | |||||||||||||||||
| Chain | 24 – 93 | 70 | SDF-1-beta(3-72) | |||||||||||||||||
| Chain | 24 – 88 | 65 | SDF-1-alpha(3-67) | |||||||||||||||||
Amino acid modifications | ||||||||||||||||||||
| Disulfide bond | 30 ↔ 55 | |||||||||||||||||||
| Disulfide bond | 32 ↔ 71 | |||||||||||||||||||
Natural variations | ||||||||||||||||||||
| Alternative sequence | 90 – 93 | 4 | Missing in isoform Alpha. | |||||||||||||||||
Secondary structure | ||||||||||||||||||||
Helix Strand Turn | ||||||||||||||||||||
| Beta strand | 25 – 28 | 4 | ||||||||||||||||||
| Helix | 41 – 43 | 3 | ||||||||||||||||||
| Beta strand | 44 – 52 | 9 | ||||||||||||||||||
| Turn | 53 – 55 | 3 | ||||||||||||||||||
| Beta strand | 56 – 63 | 8 | ||||||||||||||||||
| Turn | 64 – 66 | 3 | ||||||||||||||||||
| Beta strand | 69 – 72 | 4 | ||||||||||||||||||
| Helix | 77 – 85 | 9 | ||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | Spotila L.D. Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. |
| [2] | "Structure and chromosomal localization of the human stromal cell-derived factor 1 (SDF1) gene." Shirozu M., Nakano T., Inazawa J., Tashiro K., Tada H., Shinohara T., Honjo T. Genomics 28:495-500(1995) [PubMed: 7490086] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. |
| [3] | "Nucleotide sequence of hIRH, human intercrine reduced in hepatomas." Begum N.A., Barnard G.F. Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA). Tissue: Liver. |
| [4] | SeattleSNPs program for genomic applications Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. |
| [5] | "The DNA sequence and comparative analysis of human chromosome 10." Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. Rogers J.Nature 429:375-381(2004) [PubMed: 15164054] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM ALPHA). Tissue: Brain. |
| [7] | "Differential processing of stromal-derived factor-1alpha and beta explains functional diversity." De La Luz Sierra M., Yang F., Narazaki M., Salvucci O., Davis D., Yarchoan R., Zhang H.H., Fales H., Tosato G. Blood 103:2452-2459(2004) [PubMed: 14525775] [Abstract] Cited for: IDENTIFICATION OF SDF-1ALPHA(3-67) AND SDF-1BETA(3-72) BY MASS SPECTROMETRY, PROTEOLYTIC PROCESSING OF N-TERMINAL AND C-TERMINAL. |
| [8] | "Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1." Crump M.P., Gong J.H., Loetscher P., Rajarathnam K., Amara A., Arenzana-Seisdedos F., Virelizier J.-L., Baggiolini M., Sykes B.D., Clark-Lewis I. EMBO J. 16:6996-7007(1997) [PubMed: 9384579] [Abstract] Cited for: STRUCTURE BY NMR OF 22-88. |
| [9] | "Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1alpha, a potent ligand for the HIV-1 'fusin' coreceptor." Dealwis C., Fernandez E.J., Thompson D.A., Simon R.J., Siani M.A., Lolis E. Proc. Natl. Acad. Sci. U.S.A. 95:6941-6946(1998) [PubMed: 9618518] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 22-88. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| U16752 mRNA. Translation: AAA97434.1. L36033 mRNA. Translation: AAB39332.1. L36034 mRNA. Translation: AAB39333.1. U19495 mRNA. Translation: AAB40516.1. AY802782 Genomic DNA. Translation: AAV49999.1. AL137026 Genomic DNA. Translation: CAC10203.1. BC039893 mRNA. Translation: AAH39893.1. | |||||||||||||||||||||||||||||||||||||||||||||||||
| PIR | G01540. | ||||||||||||||||||||||||||||||||||||||||||||||||
| RefSeq | NP_000600.1. NP_954637.1. | ||||||||||||||||||||||||||||||||||||||||||||||||
| UniGene | Hs.522891 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D structure databases | |||||||||||||||||||||||||||||||||||||||||||||||||
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| ModBase | Search... | ||||||||||||||||||||||||||||||||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||||||||||||||||||||||||||||||||
| DIP | DIP:391N. DIP:5895N. | ||||||||||||||||||||||||||||||||||||||||||||||||
Genome annotation databases | |||||||||||||||||||||||||||||||||||||||||||||||||
| Ensembl | ENSG00000107562. Homo sapiens. [Contig view] | ||||||||||||||||||||||||||||||||||||||||||||||||
| GeneID | 6387. | ||||||||||||||||||||||||||||||||||||||||||||||||
| KEGG | hsa:6387. | ||||||||||||||||||||||||||||||||||||||||||||||||
Organism-specific databases | |||||||||||||||||||||||||||||||||||||||||||||||||
| H-InvDB | HIX0008784. | ||||||||||||||||||||||||||||||||||||||||||||||||
| HGNC | HGNC:10672. CXCL12. | ||||||||||||||||||||||||||||||||||||||||||||||||
| HPA | CAB017564. | ||||||||||||||||||||||||||||||||||||||||||||||||
| MIM | 600835. gene. | ||||||||||||||||||||||||||||||||||||||||||||||||
| PharmGKB | PA35602. | ||||||||||||||||||||||||||||||||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||||||||||||||||||||||||||||||||
| GeneCards | Search... | ||||||||||||||||||||||||||||||||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||||||||||||||||||||||||||||||||
| HOVERGEN | P48061. | ||||||||||||||||||||||||||||||||||||||||||||||||
Gene expression databases | |||||||||||||||||||||||||||||||||||||||||||||||||
| ArrayExpress | P48061. | ||||||||||||||||||||||||||||||||||||||||||||||||
| CleanEx | HS_CXCL12. | ||||||||||||||||||||||||||||||||||||||||||||||||
| GermOnline | ENSG00000107562. Homo sapiens. | ||||||||||||||||||||||||||||||||||||||||||||||||
Family and domain databases | |||||||||||||||||||||||||||||||||||||||||||||||||
| InterPro | IPR002473. C-X-C/Interlkn_8. IPR001811. Chemokine_IL8. IPR001089. CXC_chmkine_smll. [Graphical view] | ||||||||||||||||||||||||||||||||||||||||||||||||
| Pfam | PF00048. IL8. 1 hit. [Graphical view] | ||||||||||||||||||||||||||||||||||||||||||||||||
| PRINTS | PR00436. INTERLEUKIN8. | ||||||||||||||||||||||||||||||||||||||||||||||||
| SMART | SM00199. SCY. 1 hit. [Graphical view] | ||||||||||||||||||||||||||||||||||||||||||||||||
| PROSITE | PS00471. SMALL_CYTOKINES_CXC. False negative. [Graphical view] | ||||||||||||||||||||||||||||||||||||||||||||||||
| ProDom | P48061. [Graphical view] [Entries sharing at least one domain] | ||||||||||||||||||||||||||||||||||||||||||||||||
| BLOCKS | Search... | ||||||||||||||||||||||||||||||||||||||||||||||||
Other Resources | |||||||||||||||||||||||||||||||||||||||||||||||||
| DrugBank | DB01234. Dexamethasone. | ||||||||||||||||||||||||||||||||||||||||||||||||
| LinkHub | P48061. | ||||||||||||||||||||||||||||||||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||||||||||||||||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||||||||||||||||||||||||||||||||
Entry information
| Entry name | SDF1_HUMAN | ||||||||
| Accession | Primary (citable) accession number: P48061 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
Relevant documents
| Human chromosome 10 Human chromosome 10: entries, gene names and cross-references to MIM |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with


