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Yorodumi- PDB-2k03: Structure of SDF1 in complex with the CXCR4 N-terminus containing... -
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-Basic information
Entry | Database: PDB / ID: 2k03 | ||||||
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Title | Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21 | ||||||
Components |
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Keywords | CYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / CXCR4 / chemokine / sulfotyrosine / locked dimer / Alternative splicing / Chemotaxis / Growth factor / Secreted / G-protein coupled receptor / Glycoprotein / Host-virus interaction / Membrane / Receptor / Sulfation / Transducer / Transmembrane | ||||||
Function / homology | Function and homology information C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / regulation of actin polymerization or depolymerization / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / C-C chemokine receptor activity / endothelial tube morphogenesis / positive regulation of dopamine secretion / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / positive regulation of chemotaxis / regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / induction of positive chemotaxis / integrin activation / positive regulation of dendrite extension / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / anchoring junction / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / positive regulation of calcium ion import / epithelial cell development / cellular response to cytokine stimulus / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / regulation of calcium ion transport / positive regulation of cell adhesion / positive regulation of T cell migration / Binding and entry of HIV virion / animal organ regeneration / Nuclear signaling by ERBB4 / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / cardiac muscle contraction / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / neurogenesis / cell chemotaxis / adult locomotory behavior / response to activity / ubiquitin binding / G protein-coupled receptor activity / axon guidance / calcium-mediated signaling / brain development / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / cellular response to xenobiotic stimulus / integrin binding / late endosome / virus receptor activity / actin binding / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / collagen-containing extracellular matrix / Estrogen-dependent gene expression / lysosome / response to hypoxia / early endosome / cell adhesion / positive regulation of cell migration / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. | ||||||
Authors | Volkman, B.F. / Veldkamp, C.T. / Peterson, F.C. | ||||||
Citation | Journal: Sci.Signal. / Year: 2008 Title: Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12 Authors: Veldkamp, C.T. / Seibert, C. / Peterson, F.C. / De la Cruz, N.B. / Haugner, J.C. / Basnet, H. / Sakmar, T.P. / Volkman, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k03.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2k03.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2k03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/2k03 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/2k03 | HTTPS FTP |
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-Related structure data
Related structure data | 2k01C 2k04C 2k05C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8188.760 Da / Num. of mol.: 2 / Fragment: SDF-1-alpha(3-67) domain / Mutation: L36C,A65C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / Strain (production host): SD13009[pREP4] / References: UniProt: P48061 #2: Protein/peptide | Mass: 4598.835 Da / Num. of mol.: 2 / Fragment: N-terminus, residues 1-38 / Mutation: C28A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR4 / Production host: Escherichia coli (E. coli) / Strain (production host): SD13009[pREP4] / References: UniProt: P61073 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 21 / pH: 6.8 / Pressure: AMBIENT / Temperature: 308 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. Software ordinal: 1 Details: CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2070 NOE CONSTRAINTS (728 INTRA, 470 SEQUENTIAL, 246 MEDIUM, 418 LONG RANGE, 116 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), ...Details: CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2070 NOE CONSTRAINTS (728 INTRA, 470 SEQUENTIAL, 246 MEDIUM, 418 LONG RANGE, 116 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 92 INTERMOLECULAR CONSTRAINTS (CXCL12 TO CXCR4)) AND 128 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |