+Open data
-Basic information
Entry | Database: PDB / ID: 2ked | ||||||
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Title | Structure of SDF-1/CXCL12 | ||||||
Components | Stromal cell-derived factor 1-alpha | ||||||
Keywords | CYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / chemokine / Alternative splicing / Chemotaxis / Growth factor / Secreted | ||||||
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 / molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Volkman, B.F. / Veldkamp, C.T. / Peterson, F.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Monomeric structure of the cardioprotective chemokine SDF-1/CXCL12 Authors: Veldkamp, C.T. / Ziarek, J.J. / Su, J. / Basnet, H. / Lennertz, R. / Weiner, J.J. / Peterson, F.C. / Baker, J.E. / 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 | 2ked.cif.gz | 488.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ked.ent.gz | 415.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ked.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/2ked ftp://data.pdbj.org/pub/pdb/validation_reports/ke/2ked | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8166.709 Da / Num. of mol.: 1 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) / 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
Details | Contents: 1.6 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.6 mM / Component: CXCL12/SDF1-alpha-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.001 / pH: 5.5 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, CXCL12 STRUCTURES ...Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, CXCL12 STRUCTURES ARE BASED ON A TOTAL OF 1221 NOE CONSTRAINTS ( 371 INTRA, 239 SEQUENTIAL, 219 MEDIUM, 392 LONG RANGE) AND 66 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |