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Yorodumi- PDB-2sdf: SOLUTION NMR STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2sdf | ||||||
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Title | SOLUTION NMR STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), 30 STRUCTURES | ||||||
Components | STROMAL CELL-DERIVED FACTOR-1Stromal cell-derived factor 1 | ||||||
Keywords | CYTOKINE / SDF-1 / CHEMOKINES / STROMAL CELL-DERIVED FACTOR-1 / G-COUPLED RECEPTORS / PROTEIN SYNTHESIS / SOLUTION STRUCTURE | ||||||
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 / positive regulation of monocyte chemotaxis / blood circulation / 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 / detection of mechanical stimulus involved in sensory perception of pain / Nuclear signaling by ERBB4 / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / adult locomotory behavior / cell chemotaxis / axon guidance / neuron migration / growth factor activity / response to virus / response to peptide hormone / defense response / intracellular calcium ion homeostasis / 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 / simulated annealing | ||||||
Authors | Crump, M.P. / Rajarathnam, K. / Clark-Lewis, I. / Sykes, B.D. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1. Authors: Crump, M.P. / Gong, J.H. / Loetscher, P. / Rajarathnam, K. / Amara, A. / Arenzana-Seisdedos, F. / Virelizier, J.L. / Baggiolini, M. / Sykes, B.D. / Clark-Lewis, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2sdf.cif.gz | 645.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2sdf.ent.gz | 562.2 KB | Display | PDB format |
PDBx/mmJSON format | 2sdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/2sdf ftp://data.pdbj.org/pub/pdb/validation_reports/sd/2sdf | 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: 7849.280 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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 | pH: 4.9 / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: STRUCTURES WERE REFINED WITH MULTIPLE ROUNDS OF SIMULATED ANNEALING, WITH THE ADDITION OF NEW NOES AND CORRECTION OF AMBIGUOUS NOES. DETAILS OF THE NUMBER OF RESTRAINTS ETC. CAN BE FOUND IN ...Details: STRUCTURES WERE REFINED WITH MULTIPLE ROUNDS OF SIMULATED ANNEALING, WITH THE ADDITION OF NEW NOES AND CORRECTION OF AMBIGUOUS NOES. DETAILS OF THE NUMBER OF RESTRAINTS ETC. CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||
NMR ensemble | Conformer selection criteria: ENSEMBLE OF 30 STRUCTURES THAT SATISFIED THE NMR RESTRAINTS WITH NO NOE VIOLATIONS GREATER THAN 0.3 A AND NO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 3 DEGREES. Conformers calculated total number: 30 / Conformers submitted total number: 30 |