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Open data
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Basic information
Entry | Database: PDB / ID: 2k01 | ||||||
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Title | Structure of a locked SDF1 dimer | ||||||
![]() | Stromal cell-derived factor 1 | ||||||
![]() | CYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / chemokine / sulfotyrosine / locked dimer / Alternative splicing / Chemotaxis / Growth factor / Secreted | ||||||
Function / homology | ![]() 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 / growth factor activity / neuron migration / 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 / cell adhesion / response to hypoxia / 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 | ![]() | ||||||
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, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | ||||||
![]() | Volkman, B.F. / Veldkamp, C.T. / Peterson, F.C. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 970.2 KB | Display | ![]() |
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PDB format | ![]() | 824.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 486.8 KB | Display | ![]() |
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Full document | ![]() | 910.2 KB | Display | |
Data in XML | ![]() | 66.7 KB | Display | |
Data in CIF | ![]() | 94.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2k03C ![]() 2k04C ![]() 2k05C C: citing same article ( |
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Similar structure data | |
Other databases |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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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.) ![]() ![]() ![]() |
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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: 0.620 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.: 0.620 mM / Component: CXCL12/SDF1-alpha / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 21 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / 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, AUTOMATED METHODS WERE ...Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, 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 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND ...Details: CXCL12 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 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., CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 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 |