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P48061 (SDF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 150. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Stromal cell-derived factor 1

Short name=SDF-1
Short name=hSDF-1
Alternative name(s):
C-X-C motif chemokine 12
Intercrine reduced in hepatomas
Short name=IRH
Short name=hIRH
Pre-B cell growth-stimulating factor
Short name=PBSF

Cleaved into the following 2 chains:

  1. SDF-1-beta(3-72)
  2. SDF-1-alpha(3-67)
Gene names
Name:CXCL12
Synonyms:SDF1, SDF1A, SDF1B
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length93 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Chemoattractant active on T-lymphocytes, monocytes, but not neutrophils. Activates the C-X-C chemokine receptor CXCR4 to induce a rapid and transient rise in the level of intracellular calcium ions and chemotaxis. Also binds to atypical chemokine receptor ACKR3, which activates the beta-arrestin pathway and acts as a scavenger receptor for SDF-1. 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. Acts as a positive regulator of monocyte migration and a negative regulator of monocyte adhesion via the LYN kinase. Stimulates migration of monocytes and T-lymphocytes through its receptors, CXCR4 and ACKR3, and decreases monocyte adherence to surfaces coated with ICAM-1, a ligand for beta-2 integrins. SDF1A/CXCR4 signaling axis inhibits beta-2 integrin LFA-1 mediated adhesion of monocytes to ICAM-1 through LYN kinase. Inhibits CXCR4-mediated infection by T-cell line-adapted HIV-1. Plays a protective role after myocardial infarction. Induces down-regulation and internalization of ACKR3 expressed in various cells. Has several critical functions during embryonic development; required for B-cell lymphopoiesis, myelopoiesis in bone marrow and heart ventricular septum formation. Ref.13 Ref.16 Ref.17 Ref.19 Ref.22 Ref.23

Subunit structure

Monomer or homodimer; in equilibrium. Dimer formation is induced by non acidic pH and the presence of multivalent anions, and by binding to CXCR4 or heparin. Monomeric form is required for full chemotactic activity and resistance to ischemia/reperfusion injury, whereas the dimeric form acts as a partial agonist of CXCR4, stimulating Ca2+ mobilization but with no chemotactic activity and instead acts as a selective antagonist that blocks chemotaxis induced by the monomeric form. Interacts with the N-terminus of ACKR3. Ref.14 Ref.15 Ref.19 Ref.20 Ref.21 Ref.23 Ref.24 Ref.31 Ref.32 Ref.34

Subcellular location

Secreted.

Tissue specificity

Isoform Alpha and isoform Beta are ubiquitously expressed, with highest levels detected in liver, pancreas and spleen. Isoform Gamma is mainly expressed in heart, with weak expression detected in several other tissues. Isoform Delta, isoform Epsilon and isoform Theta have highest expression levels in pancreas, with lower levels detected in heart, kidney, liver and spleen. Ref.2

Developmental stage

Isoform Alpha is ubiquitously expressed in fetal tissues. Isoform Beta and isoform Delta have more limited expression patterns, with highest levels detected in fetal spleen and fetal liver, respectively. Isoform Gamma and isoform Theta are weakly detected in fetal kidney. Ref.2

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 processed at the N-terminus. The C-terminal processing of isoform Alpha is reduced by binding to heparin and, probably, cell surface proteoglycans. Ref.18

Sequence similarities

Belongs to the intercrine alpha (chemokine CxC) family.

Mass spectrometry

Isoform Alpha: Molecular mass is 7959 Da from positions 22 - 89. Determined by ESI. Ref.18

Isoform Alpha: Molecular mass is 7606 Da from positions 24 - 88. Determined by ESI. Ref.18

Isoform Beta: Molecular mass is 8522 Da from positions 22 - 93. Determined by ESI. Ref.18

Isoform Beta: Molecular mass is 8297 Da from positions 24 - 93. Determined by ESI. Ref.18

Sequence caution

The sequence CAC10202.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
   Biological processChemotaxis
   Cellular componentSecreted
   Coding sequence diversityAlternative splicing
   DomainSignal
   Molecular functionCytokine
Growth factor
   PTMDisulfide bond
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processG-protein coupled receptor signaling pathway

Traceable author statement PubMed 8752280. Source: ProtInc

T cell proliferation

Inferred from electronic annotation. Source: Ensembl

adult locomotory behavior

Inferred from electronic annotation. Source: Ensembl

ameboidal cell migration

Inferred from electronic annotation. Source: Ensembl

blood circulation

Traceable author statement PubMed 10772939. Source: ProtInc

cell adhesion

Traceable author statement PubMed 10198043. Source: ProtInc

cellular calcium ion homeostasis

Traceable author statement PubMed 10772939. Source: ProtInc

chemokine-mediated signaling pathway

Inferred from direct assay PubMed 20388803. Source: BHF-UCL

germ cell development

Inferred from electronic annotation. Source: Ensembl

germ cell migration

Inferred from electronic annotation. Source: Ensembl

immune response

Traceable author statement PubMed 10802710. Source: ProtInc

induction of positive chemotaxis

Inferred from electronic annotation. Source: Ensembl

motor neuron axon guidance

Inferred from electronic annotation. Source: Ensembl

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage

Inferred from direct assay PubMed 20388803. Source: BHF-UCL

negative regulation of leukocyte apoptotic process

Inferred from direct assay PubMed 15059845. Source: BHF-UCL

neuron migration

Inferred from electronic annotation. Source: Ensembl

organ regeneration

Inferred from electronic annotation. Source: Ensembl

patterning of blood vessels

Inferred from electronic annotation. Source: Ensembl

positive regulation of axon extension involved in axon guidance

Inferred from electronic annotation. Source: Ensembl

positive regulation of dopamine secretion

Inferred from electronic annotation. Source: Ensembl

positive regulation of endothelial cell proliferation

Inferred from electronic annotation. Source: Ensembl

positive regulation of monocyte chemotaxis

Inferred from direct assay Ref.22. Source: UniProtKB

positive regulation of neuron differentiation

Inferred from electronic annotation. Source: Ensembl

regulation of actin polymerization or depolymerization

Traceable author statement PubMed 10570282. Source: ProtInc

regulation of calcium ion transport

Inferred from electronic annotation. Source: Ensembl

response to heat

Inferred from electronic annotation. Source: Ensembl

response to hypoxia

Inferred from electronic annotation. Source: Ensembl

response to mechanical stimulus

Inferred from electronic annotation. Source: Ensembl

response to peptide hormone

Inferred from electronic annotation. Source: Ensembl

response to radiation

Inferred from electronic annotation. Source: Ensembl

response to virus

Traceable author statement PubMed 10772939. Source: ProtInc

telencephalon cell migration

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentexternal side of plasma membrane

Inferred from electronic annotation. Source: Ensembl

extracellular region

Traceable author statement. Source: Reactome

extracellular space

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionCXCR chemokine receptor binding

Inferred from direct assay PubMed 20388803. Source: BHF-UCL

chemokine activity

Traceable author statement PubMed 12782716. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 6 isoforms produced by alternative splicing. [Align] [Select]
Isoform Beta (identifier: P48061-1)

Also known as: SDF-1-beta(1-72); hSDF-1beta;

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); hSDF-1alpha;

The sequence of this isoform differs from the canonical sequence as follows:
     90-93: Missing.
Isoform Gamma (identifier: P48061-3)

Also known as: hSDF-1gamma; SDF-1g;

The sequence of this isoform differs from the canonical sequence as follows:
     90-93: RFKM → GRREEKVGKKEKIGKKKRQKKRKAAQKRKN
Isoform Delta (identifier: P48061-4)

Also known as: hSDF-1delta;

The sequence of this isoform differs from the canonical sequence as follows:
     89-93: KRFKM → NLISAAPAGKRVIAGARALHPSPPRACPTARALCEIRLWPPPEWSWPSPGDV
Isoform Epsilon (identifier: P48061-5)

Also known as: hSDFepsilon;

The sequence of this isoform differs from the canonical sequence as follows:
     89-93: KRFKM → NC
Isoform Theta (identifier: P48061-6)

Also known as: hSDFphi; hSDFtheta; Phi;

The sequence of this isoform differs from the canonical sequence as follows:
     90-93: RFKM → IWLYGNAETSR

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2121 Potential
Chain22 – 9372Stromal cell-derived factor 1
PRO_0000005109
Chain24 – 9370SDF-1-beta(3-72)
PRO_0000005110
Chain24 – 8865SDF-1-alpha(3-67)
PRO_0000005111

Regions

Region29 – 335Receptor and heparin binding Probable
Region39 – 413Receptor binding
Region41 – 5111Heparin binding
Region48 – 503Receptor binding
Region60 – 7011Receptor binding
Motif22 – 232Receptor activation motif

Sites

Binding site621Heparin
Binding site691Heparin
Binding site851Heparin
Site461Important for dimer formation

Amino acid modifications

Disulfide bond30 ↔ 55 Ref.25 Ref.26 Ref.27 Ref.28 Ref.29 Ref.30 Ref.31 Ref.32 Ref.33
Disulfide bond32 ↔ 71 Ref.25 Ref.26 Ref.27 Ref.28 Ref.29 Ref.30 Ref.31 Ref.32 Ref.33

Natural variations

Alternative sequence89 – 935KRFKM → NLISAAPAGKRVIAGARALH PSPPRACPTARALCEIRLWP PPEWSWPSPGDV in isoform Delta.
VSP_042118
Alternative sequence89 – 935KRFKM → NC in isoform Epsilon.
VSP_042119
Alternative sequence90 – 934Missing in isoform Alpha.
VSP_001056
Alternative sequence90 – 934RFKM → GRREEKVGKKEKIGKKKRQK KRKAAQKRKN in isoform Gamma.
VSP_041209
Alternative sequence90 – 934RFKM → IWLYGNAETSR in isoform Theta.
VSP_042120

Experimental info

Mutagenesis22 – 232Missing: Abolished CXCR4 activation ability, but only slightly impaired binding to the receptor. Ref.25 Ref.30
Mutagenesis221K → A: Loss of chemotactic activity. Ref.25 Ref.30
Mutagenesis221K → R: Abolished CXCR4 activation ability, but only slightly impaired binding to the receptor. Ref.25 Ref.30
Mutagenesis221Missing: Abolished CXCR4 activation ability, but only slightly impaired binding to the receptor. Ref.25 Ref.30
Mutagenesis231P → G: Abolished CXCR4 activation ability, but only slightly impaired binding to the receptor. Ref.25
Mutagenesis25 – 273SLS → AQA: Significantly impaired CXCR4 activation ability, but only slightly impaired binding to the receptor. Ref.25
Mutagenesis281Y → A: Impaired CXCR4 activation ability, but only slightly impaired binding to the receptor. Ref.25
Mutagenesis281Y → H: No significant effect on CXCR4 binding or activation. Ref.25
Mutagenesis291R → K: Slightly impaired binding and activation of CXCR4. Ref.25 Ref.29
Mutagenesis291R → Q: Greatly impaired chemotactic activity and enhanced inhibition by heparin. Ref.25 Ref.29
Mutagenesis33 – 386RFFESH → AAAAAA: Significantly decreased chemotactic activity. Ref.27 Ref.29
Mutagenesis331R → A: Significantly decreased anti-HIV-1 and chemotactic activities. Ref.27 Ref.29
Mutagenesis331R → Q: Slightly impaired chemotactic activity and enhanced inhibition by heparin. Greatly impaired chemotactic activity; when associated with Q-29. Ref.27 Ref.29
Mutagenesis341F → A: No effect on anti-HIV-1 and chemotactic activities. Slightly impaired chemotactic activity and no effect on inhibition by heparin; when associated with A-35. Ref.27
Mutagenesis351F → A: No effect on anti-HIV-1 and chemotactic activities. Slightly impaired chemotactic activity and no effect on inhibition by heparin; when associated with A-34. Ref.27
Mutagenesis36 – 383ESH → QSN: Slightly impaired chemotactic activity, no effect on inhibition by heparin. Ref.27 Ref.29
Mutagenesis361E → A: No effect on anti-HIV-1 and chemotactic activities. Ref.27
Mutagenesis371S → A: No effect on anti-HIV-1 and chemotactic activities. Ref.27
Mutagenesis381H → A: No effect on anti-HIV-1 and chemotactic activities. Ref.27
Mutagenesis411R → A: No effect on CXCR4 activation. Ref.31
Mutagenesis45 – 484KHLK → SSLS: Loss of heparin-binding capacity. Ref.15 Ref.29 Ref.31
Mutagenesis461H → A: Reduced dimerization in neutral pH. Eliminates the pH dependence of dimerization. Ref.20 Ref.29 Ref.31
Mutagenesis461H → L: No significant effect on dimerization in neutral pH. Eliminates the pH dependence of dimerization. Ref.20 Ref.29 Ref.31
Mutagenesis461H → N: Slightly impaired CXCR4 activation and clear resistance to inhibition by heparin; when associated with Q-48; Q-62; Q-68 and N-69. Ref.20 Ref.29 Ref.31
Mutagenesis461H → R: No effect on CXCR4 activation. Impaired dimer formation, leading to increased chemotactic activity. Eliminates the pH dependence of dimerization. Ref.20 Ref.29 Ref.31
Mutagenesis481K → A: Impaired CXCR4 activation. Ref.29 Ref.31
Mutagenesis481K → E: Impaired CXCR4 activation. Ref.29 Ref.31
Mutagenesis481K → Q: Slightly impaired CXCR4 activation and clear resistance to inhibition by heparin; when associated with N-46; Q-62; Q-68 and N-69. Ref.29 Ref.31
Mutagenesis52 – 565TPNCA → GPGCG: Slightly impaired chemotactic activity, no effect on inhibition by heparin. Ref.29
Mutagenesis571L → C: Formation of an intermolecular disulfide bond, leading to a locked dimer; when associated with C-86. No effect on CXCR4 activation, but loss of chemotactic activity; when associated with C-86.
Mutagenesis601V → A: Impaired CXCR4 activation. Ref.31
Mutagenesis621R → A: No effect on CXCR4 activation. Ref.29 Ref.31
Mutagenesis621R → Q: Slightly impaired CXCR4 activation and clear resistance to inhibition by heparin; when associated with N-46; Q-48; Q-68 and N-69. Ref.29 Ref.31
Mutagenesis681R → A: Impaired CXCR4 activation. Ref.29 Ref.31
Mutagenesis681R → E: Greatly impaired CXCR4 activation. Ref.29 Ref.31
Mutagenesis681R → Q: Slightly impaired CXCR4 activation and clear resistance to inhibition by heparin; when associated with N-46; Q-48; Q-62 and N-69. Ref.29 Ref.31
Mutagenesis691Q → N: Slightly impaired CXCR4 activation and clear resistance to inhibition by heparin; when associated with N-46; Q-48; Q-62 and Q-68. Ref.29
Mutagenesis701V → A: Impaired CXCR4 activation. Ref.31
Mutagenesis811E → A: No effect on CXCR4 activation. Ref.31
Mutagenesis841E → A: No effect on CXCR4 activation. Ref.31
Mutagenesis851K → A: No effect on CXCR4 activation. Ref.31
Mutagenesis861A → C: Formation of an intermolecular disulfide bond, leading to a locked dimer; when associated with C-57. No effect on CXCR4 activation, but loss of chemotactic activity; when associated with C-57.

Secondary structure

.................... 93
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Beta (SDF-1-beta(1-72)) (hSDF-1beta) [UniParc].

Last modified February 1, 1996. Version 1.
Checksum: 505B5A29C2B44E8D

FASTA9310,666
        10         20         30         40         50         60 
MNAKVVVVLV LVLTALCLSD GKPVSLSYRC PCRFFESHVA RANVKHLKIL NTPNCALQIV 

        70         80         90 
ARLKNNNRQV CIDPKLKWIQ EYLEKALNKR FKM 

« Hide

Isoform Alpha (SDF-1-alpha(1-68)) (hSDF-1alpha) [UniParc].

Checksum: 62B44E8D209C3A14
Show »

FASTA8910,103
Isoform Gamma (hSDF-1gamma) (SDF-1g) [UniParc].

Checksum: C36297D68341B824
Show »

FASTA11913,705
Isoform Delta (hSDF-1delta) [UniParc].

Checksum: 602BFEB309014ED2
Show »

FASTA14015,495
Isoform Epsilon (hSDFepsilon) [UniParc].

Checksum: 7375C44E8D209C3A
Show »

FASTA9010,192
Isoform Theta (hSDFphi) (hSDFtheta) (Phi) [UniParc].

Checksum: BEF2739B8E70BAAD
Show »

FASTA10011,395

References

« Hide 'large scale' references
[1]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS ALPHA AND BETA).
[2]"Identification and expression of novel isoforms of human stromal cell-derived factor 1."
Yu L., Cecil J., Peng S.B., Schrementi J., Kovacevic S., Paul D., Su E.W., Wang J.
Gene 374:174-179(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS GAMMA; DELTA; EPSILON AND THETA), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, ALTERNATIVE SPLICING.
Tissue: Fetal brain, Fetal heart and Heart.
[3]Spotila L.D.
Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM BETA).
Tissue: Fibroblast.
[4]"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.
[5]"Inhibition of X4 and R5 HIV-1 by human SDF-1g, a novel chemokine that interferes with HIV transcription."
Callebaut C., Verdin E.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM GAMMA).
[6]"Polymorphism study of cell-derived factor 1 (SDF1) gene and their correlation with HIV infection in a Chinese cohort."
Zhao X., Zhang H., Lee S., Wong K., Zheng B.
Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA).
[7]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM ALPHA).
[8]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS ALPHA AND BETA).
Tissue: Thymus and Uterus.
[9]SeattleSNPs variation discovery resource
Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[10]"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. expand/collapse author list , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[11]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[12]"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] (ISOFORM ALPHA).
Tissue: Brain.
[13]"The CXC chemokine SDF-1 is the ligand for LESTR/fusin and prevents infection by T-cell-line-adapted HIV-1."
Oberlin E., Amara A., Bachelerie F., Bessia C., Virelizier J.-L., Arenzana-Seisdedos F., Schwartz O., Heard J.-M., Clark-Lewis I., Legler D.F., Loetscher M., Baggiolini M., Moser B.
Nature 382:833-835(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[14]"AMD3100, a small molecule inhibitor of HIV-1 entry via the CXCR4 co-receptor."
Donzella G.A., Schols D., Lin S.W., Este J.A., Nagashima K.A., Maddon P.J., Allaway G.P., Sakmar T.P., Henson G., De Clercq E., Moore J.P.
Nat. Med. 4:72-77(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CXCR4.
[15]"Stromal cell-derived factor-1alpha associates with heparan sulfates through the first beta-strand of the chemokine."
Amara A., Lorthioir O., Valenzuela A., Magerus A., Thelen M., Montes M., Virelizier J.L., Delepierre M., Baleux F., Lortat-Jacob H., Arenzana-Seisdedos F.
J. Biol. Chem. 274:23916-23925(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HEPARAN SULFATE, MUTAGENESIS OF 45-LYS--LYS-48.
[16]"Characterization of a Xenopus laevis CXC chemokine receptor 4: implications for hematopoietic cell development in the vertebrate embryo."
Moepps B., Braun M., Knoepfle K., Dillinger K., Knoechel W., Gierschik P.
Eur. J. Immunol. 30:2924-2934(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[17]"Xenopus laevis stromal cell-derived factor 1: conservation of structure and function during vertebrate development."
Braun M., Wunderlin M., Spieth K., Knoechel W., Gierschik P., Moepps B.
J. Immunol. 168:2340-2347(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[18]"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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION OF SDF-1ALPHA(3-67) AND SDF-1BETA(3-72) BY MASS SPECTROMETRY, PROTEOLYTIC PROCESSING OF N-TERMINUS AND C-TERMINUS.
[19]"The chemokine SDF-1/CXCL12 binds to and signals through the orphan receptor RDC1 in T lymphocytes."
Balabanian K., Lagane B., Infantino S., Chow K.Y., Harriague J., Moepps B., Arenzana-Seisdedos F., Thelen M., Bachelerie F.
J. Biol. Chem. 280:35760-35766(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH ACKR3.
[20]"The monomer-dimer equilibrium of stromal cell-derived factor-1 (CXCL 12) is altered by pH, phosphate, sulfate, and heparin."
Veldkamp C.T., Peterson F.C., Pelzek A.J., Volkman B.F.
Protein Sci. 14:1071-1081(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: DIMERIZATION, MUTAGENESIS OF HIS-46.
[21]"Recognition of a CXCR4 sulfotyrosine by the chemokine stromal cell-derived factor-1alpha (SDF-1alpha/CXCL12)."
Veldkamp C.T., Seibert C., Peterson F.C., Sakmar T.P., Volkman B.F.
J. Mol. Biol. 359:1400-1409(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: DIMERIZATION, INTERACTION WITH CXCR4.
[22]"Monocyte migration and LFA-1-mediated attachment to brain microvascular endothelia is regulated by SDF-1 alpha through Lyn kinase."
Malik M., Chen Y.-Y., Kienzle M.F., Tomkowicz B.E., Collman R.G., Ptasznik A.
J. Immunol. 181:4632-4637(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[23]"AMD3100 is a CXCR7 ligand with allosteric agonist properties."
Kalatskaya I., Berchiche Y.A., Gravel S., Limberg B.J., Rosenbaum J.S., Heveker N.
Mol. Pharmacol. 75:1240-1247(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH ACKR3.
[24]"Ubiquitination of CXCR7 controls receptor trafficking."
Canals M., Scholten D.J., de Munnik S., Han M.K., Smit M.J., Leurs R.
PLoS ONE 7:E34192-E34192(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: RECEPTOR INTERACTION.
[25]"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] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 22-88, DISULFIDE BONDS, MUTAGENESIS OF LYS-22; PRO-23; 22-LYS-PRO-23; 25-SER--SER-27; TYR-28 AND ARG-29.
[26]"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 22-88 OF MUTANT ALA-54, DISULFIDE BONDS.
[27]"Crystal structure of recombinant native SDF-1alpha with additional mutagenesis studies: an attempt at a more comprehensive interpretation of accumulated structure-activity relationship data."
Ohnishi Y., Senda T., Nandhagopal N., Sugimoto K., Shioda T., Nagal Y., Mitsui Y.
J. Interferon Cytokine Res. 20:691-700(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 22-88, DISULFIDE BONDS, MUTAGENESIS OF ARG-33; PHE-34; PHE-35; GLU-36; SER-37; HIS-38 AND 33-ARG--HIS-38.
[28]"Mapping the binding of the N-terminal extracellular tail of the CXCR4 receptor to stromal cell-derived factor-1alpha."
Gozansky E.K., Louis J.M., Caffrey M., Clore G.M.
J. Mol. Biol. 345:651-658(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 22-89, DISULFIDE BONDS.
[29]"Structural and functional basis of CXCL12 (stromal cell-derived factor-1 alpha) binding to heparin."
Murphy J.W., Cho Y., Sachpatzidis A., Fan C., Hodsdon M.E., Lolis E.
J. Biol. Chem. 282:10018-10027(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) OF 22-88 IN COMPLEX WITH HEPARIN DISACCHARIDE I-S, DISULFIDE BONDS, MUTAGENESIS OF ARG-29; ARG-33; 34-PHE-PHE-35; 36-GLU--HIS-38; HIS-46; LYS-48; 52-THR--ALA-56; ARG-62; ARG-68 AND GLN-69.
[30]"Crystal structure of recombinant human stromal cell-derived factor-1alpha."
Ryu E.K., Kim T.G., Kwon T.H., Jung I.D., Ryu D., Park Y.M., Kim J., Ahn K.H., Ban C.
Proteins 67:1193-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 22-89, DISULFIDE BONDS, MUTAGENESIS OF LYS-22.
[31]"Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12."
Veldkamp C.T., Seibert C., Peterson F.C., De la Cruz N.B., Haugner J.C. III, Basnet H., Sakmar T.P., Volkman B.F.
Sci. Signal. 1:RA4-RA4(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 22-89 OF MUTANT CYS-57 AND CYS-86 IN COMPLEX WITH CXCR4 FRAGMENT, SUBUNIT, DIMERIZATION, DISULFIDE BONDS, MUTAGENESIS OF ARG-41; HIS-46; LYS-48; VAL-60; ARG-62; ARG-68; VAL-70; GLU-81; GLU-84 AND LYS-85.
[32]"Monomeric structure of the cardioprotective chemokine SDF-1/CXCL12."
Veldkamp C.T., Ziarek J.J., Su J., Basnet H., Lennertz R., Weiner J.J., Peterson F.C., Baker J.E., Volkman B.F.
Protein Sci. 18:1359-1369(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 22-89, ASSAY ON RAT ISCHEMIA/REPERFUSION MODEL, DIMERIZATION, DISULFIDE BONDS.
[33]"Solution structure of human SDF1-alpha H25R."
Ziarek J.J., Veldkamp C.T., Peterson F.C., Volkman B.F.
Submitted (SEP-2009) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 22-89, DISULFIDE BONDS.
[34]"Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family."
Murphy J.W., Yuan H., Kong Y., Xiong Y., Lolis E.J.
Proteins 78:1331-1337(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 22-88, DIMERIZATION.
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L36033 mRNA. Translation: AAB39332.1.
L36034 mRNA. Translation: AAB39333.1.
DQ345517 mRNA. Translation: ABC69270.1.
DQ345518 mRNA. Translation: ABC69271.1.
DQ345519 mRNA. Translation: ABC69272.1.
DQ345520 mRNA. Translation: ABC69273.1.
U16752 mRNA. Translation: AAA97434.1.
U19495 mRNA. Translation: AAB40516.1.
AY644456 mRNA. Translation: AAT76437.1.
AY874118 mRNA. Translation: AAW82036.1.
CR450283 mRNA. Translation: CAG29279.1.
AK292628 mRNA. Translation: BAF85317.1.
AK311814 mRNA. Translation: BAG34757.1.
AY802782 Genomic DNA. Translation: AAV49999.1.
AL137026 Genomic DNA. Translation: CAC10202.1. Sequence problems.
AL137026 Genomic DNA. Translation: CAC10203.1.
CH471160 Genomic DNA. Translation: EAW86619.1.
BC039893 mRNA. Translation: AAH39893.1.
PIRG01540.
RefSeqNP_000600.1. NM_000609.6.
NP_001029058.1. NM_001033886.2.
NP_001171605.1. NM_001178134.1.
NP_001264919.1. NM_001277990.1.
NP_954637.1. NM_199168.3.
UniGeneHs.522891.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1A15X-ray2.20A/B22-88[»]
1QG7X-ray2.00A/B22-88[»]
1SDFNMR-A22-88[»]
1VMCNMR-A22-89[»]
2J7ZX-ray1.95A/B22-89[»]
2K01NMR-A/C22-89[»]
2K03NMR-A/C22-89[»]
2K04NMR-A/C22-89[»]
2K05NMR-A/C22-89[»]
2KECNMR-A22-89[»]
2KEDNMR-A22-89[»]
2KEENMR-A22-89[»]
2KOLNMR-A22-89[»]
2NWGX-ray2.07A/B22-88[»]
2SDFNMR-A22-88[»]
3GV3X-ray1.60A26-88[»]
3HP3X-ray2.20A/B/C/D/E/F/G/H/I/J22-88[»]
4LMQX-ray2.77D/F29-89[»]
ProteinModelPortalP48061.
SMRP48061. Positions 22-89.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112288. 6 interactions.
DIPDIP-391N.
DIP-5894N.
DIP-5895N.
IntActP48061. 3 interactions.
MINTMINT-6491347.
STRING9606.ENSP00000363548.

Chemistry

DrugBankDB01234. Dexamethasone.

PTM databases

PhosphoSiteP48061.

Polymorphism databases

DMDM1352728.

Proteomic databases

PaxDbP48061.
PRIDEP48061.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000343575; ENSP00000339913; ENSG00000107562. [P48061-2]
ENST00000374426; ENSP00000363548; ENSG00000107562. [P48061-3]
ENST00000374429; ENSP00000363551; ENSG00000107562. [P48061-1]
ENST00000395794; ENSP00000379140; ENSG00000107562. [P48061-4]
ENST00000395795; ENSP00000379141; ENSG00000107562. [P48061-5]
GeneID6387.
KEGGhsa:6387.
UCSCuc001jbf.4. human. [P48061-1]
uc001jbh.3. human. [P48061-3]
uc021ppm.1. human. [P48061-4]

Organism-specific databases

CTD6387.
GeneCardsGC10M044865.
H-InvDBHIX0008784.
HGNCHGNC:10672. CXCL12.
HPACAB017564.
MIM600835. gene.
neXtProtNX_P48061.
PharmGKBPA35602.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG26489.
HOGENOMHOG000220915.
HOVERGENHBG107437.
KOK10031.
OMAWIQEYLD.
OrthoDBEOG7C5MBS.
TreeFamTF353159.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.

Gene expression databases

ArrayExpressP48061.
BgeeP48061.
CleanExHS_CXCL12.
GenevestigatorP48061.

Family and domain databases

InterProIPR001811. Chemokine_IL8-like_dom.
[Graphical view]
PfamPF00048. IL8. 1 hit.
[Graphical view]
SMARTSM00199. SCY. 1 hit.
[Graphical view]
SUPFAMSSF54117. SSF54117. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP48061.
GeneWikiStromal_cell-derived_factor-1.
GenomeRNAi6387.
NextBio24808.
PMAP-CutDBQ5IT36.
PROP48061.
SOURCESearch...

Entry information

Entry nameSDF1_HUMAN
AccessionPrimary (citable) accession number: P48061
Secondary accession number(s): B2R4G0 expand/collapse secondary AC list , E7EVL0, Q2L985, Q2L986, Q2L988, Q5IT36, Q6ICW0, Q9H554
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: March 19, 2014
This is version 150 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 10

Human chromosome 10: entries, gene names and cross-references to MIM