[English] 日本語
Yorodumi- PDB-2k04: Structure of SDF1 in complex with the CXCR4 N-terminus containing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k04 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines | ||||||
Components |
| ||||||
Keywords | CYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / CXCR4 / chemokine / 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 vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / 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 vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / 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 / endothelial tube morphogenesis / positive regulation of dopamine secretion / endothelial cell differentiation / C-C chemokine receptor activity / Signaling by ROBO receptors / regulation of chemotaxis / cellular response to organonitrogen compound / C-C chemokine binding / positive regulation of chemotaxis / Formation of definitive endoderm / induction of positive chemotaxis / positive regulation of dendrite extension / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / anchoring junction / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / epithelial cell development / positive regulation of calcium ion import / cell leading edge / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / positive regulation of cell adhesion / small molecule binding / positive regulation of T cell migration / Binding and entry of HIV virion / animal organ regeneration / regulation of cell adhesion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / Nuclear signaling by ERBB4 / cardiac muscle contraction / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / cell chemotaxis / neurogenesis / adult locomotory behavior / response to activity / ubiquitin binding / G protein-coupled receptor activity / calcium-mediated signaling / axon guidance / neuron migration / growth factor activity / response to virus / brain development / response to peptide hormone / defense response / intracellular calcium ion homeostasis / chemotaxis / cellular response to xenobiotic stimulus / integrin binding / late endosome / virus receptor activity / positive regulation of cold-induced thermogenesis / actin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / collagen-containing extracellular matrix / Estrogen-dependent gene expression / lysosome / early endosome / response to hypoxia / cell adhesion / positive regulation of cell migration / inflammatory response / immune 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2k04.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2k04.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2k04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/2k04 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/2k04 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2k01C 2k03C 2k05C C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-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: 4518.772 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 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
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 |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2012 NOE CONSTRAINTS ( 744 INTRA, 384 SEQUENTIAL, 238 MEDIUM, 444 LONG RANGE, 110 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), ...Details: CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2012 NOE CONSTRAINTS ( 744 INTRA, 384 SEQUENTIAL, 238 MEDIUM, 444 LONG RANGE, 110 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 |