+Open data
-Basic information
Entry | Database: PDB / ID: 1vmc | ||||||
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Title | STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA) | ||||||
Components | Stromal cell-derived factor 1 | ||||||
Keywords | CYTOKINE / CXC-CHEMOKINE | ||||||
Function / homology | Function and homology information chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / 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 / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / axon guidance / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Gozansky, E.K. / Clore, G.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Mapping the binding of the N-terminal extracellular tail of the CXCR4 receptor to stromal cell-derived factor-1alpha. Authors: Gozansky, E.K. / Louis, J.M. / Caffrey, M. / Clore, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vmc.cif.gz | 33.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vmc.ent.gz | 22.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/1vmc ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vmc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8343.800 Da / Num. of mol.: 1 / Fragment: SDF-1ALPHA (residues 22-89) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P48061 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | Ionic strength: 50 mM SODIUM PHOSPHATE / pH: 5.5 / Temperature: 308.00 K |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 3JHN-HALPHA COUPLING CONSTANT RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT ...Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 3JHN-HALPHA COUPLING CONSTANT RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING RESTRAINTS (N-H); THE NON-BONDED INTERACTIONS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, TORSION ANGLE AND HYDROGEN BONDING DATABASE POTENTIALS OF MEAN FORCE, AND A RADIUS OF GYRATION RESTRAINT. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES BEST-FITTED TO RESIDUES 8-65. ONLY RESIDUES 8-68 ARE SHOWN SINCE RESIDUES 1-7 AT THE C-TERMINUS ARE DISORDERED IN SOLUTION EXPERIMENTAL RESTRAINTS: 562 INTERPROTON DISTANCE RESTRAINTS: (173 INTRARESIDUE; 174 SEQUENTIAL, 94 MEDIUM-RANGE, AND 121 LONG-RANGE INTERRESIDUE; 58 DISTANCE RESTRAINTS FOR 29 BACKBONE H-BONDS 202 TORSION ANGLE RESTRAINTS (69 PHI, 55 PSI, 78 CHI) 189 CALPHA/CBETA CHEMICAL SHIFT RESTRAINTS 37 3JHN-HA COUPLING CONSTANT RESTRAINTS 35 RESIDUAL NH DIPOLAR COUPLING RESTRAINTS 135 CA/CB 13C SHIFTS DIPOLAR COUPLING R-FACTOR: 5.5% (DA = -9.7Hz, RHOMBICITY = 0.46) | ||||||||||||
NMR ensemble | Conformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE Conformers calculated total number: 100 / Conformers submitted total number: 1 |