+Open data
-Basic information
Entry | Database: PDB / ID: 2kol | ||||||
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Title | Solution structure of human SDF1-alpha H25R | ||||||
Components | Stromal cell-derived factor 1 | ||||||
Keywords | CYTOKINE / chemokine / SDF1-alpha / Chemotaxis / Growth factor | ||||||
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 / detection of temperature stimulus involved in sensory perception of pain / positive regulation of calcium ion import / 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 / adult locomotory behavior / cell chemotaxis / 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 / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Volkman, B.F. / Ziarek, J.J. / Peterson, F.C. / Veldkamp, C.T. | ||||||
Citation | Journal: To be Published Title: Solution structure of human SDF1-alpha H25R Authors: Ziarek, J.J. / Veldkamp, C.T. / Peterson, F.C. / 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 | 2kol.cif.gz | 491.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kol.ent.gz | 416.9 KB | Display | PDB format |
PDBx/mmJSON format | 2kol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/2kol ftp://data.pdbj.org/pub/pdb/validation_reports/ko/2kol | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 7997.507 Da / Num. of mol.: 1 / Fragment: SDF-1-alpha, residues 22-89 / Mutation: H25R 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): SG130099[pREP4] / 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: 3.3 mM [U-100% 13C; U-100% 15N] SDF1a H25R, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 / pH: 6.8 / 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: 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: STRUCTURES ARE BASED ON A TOTAL OF 1430 NOE CONSTRAINTS (339 INTRA, 388 SEQUENTIAL, 263 MEDIUM, AND 440 LONG RANGE) AND 65 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1430 / NOE intraresidue total count: 339 / NOE long range total count: 440 / NOE medium range total count: 263 / NOE sequential total count: 388 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |