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Yorodumi- PDB-3oe9: Crystal structure of the chemokine CXCR4 receptor in complex with... -
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-Basic information
Entry | Database: PDB / ID: 3oe9 | ||||||
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Title | Crystal structure of the chemokine CXCR4 receptor in complex with a small molecule antagonist IT1t in P1 spacegroup | ||||||
Components | C-X-C chemokine receptor type 4, Lysozyme Chimera | ||||||
Keywords | SIGNALING PROTEIN / HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / 7TM / G protein-coupled receptor / GPCR / Signal transduction / chemotaxis / Cancer / HIV-1 co-receptor / Chemokine / CXCL12 / SDF1 / isothiourea / IT1t / Chimera / T4L Fusion / Membrane protein / Transmembrane / SINGNALING PROTEIN / PSI-Biology / GPCR Network | ||||||
Function / homology | Function and homology information C-X-C motif chemokine 12 receptor activity / regulation of viral process / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / C-X-C chemokine receptor activity ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / C-C chemokine receptor activity / endothelial tube morphogenesis / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / positive regulation of chemotaxis / regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / positive regulation of dendrite extension / anchoring junction / Chemokine receptors bind chemokines / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / epithelial cell development / cellular response to cytokine stimulus / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / regulation of calcium ion transport / Binding and entry of HIV virion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / cardiac muscle contraction / viral release from host cell by cytolysis / neurogenesis / cell chemotaxis / peptidoglycan catabolic process / response to activity / ubiquitin binding / G protein-coupled receptor activity / calcium-mediated signaling / brain development / neuron migration / response to virus / cellular response to xenobiotic stimulus / cell wall macromolecule catabolic process / late endosome / virus receptor activity / lysozyme / lysozyme activity / actin binding / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / host cell cytoplasm / lysosome / response to hypoxia / early endosome / positive regulation of cell migration / defense response to bacterium / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / cell surface / protein-containing complex / extracellular exosome / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo Sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Wu, B. / Mol, C.D. / Han, G.W. / Katritch, V. / Chien, E.Y.T. / Liu, W. / Cherezov, V. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR) | ||||||
Citation | Journal: Science / Year: 2010 Title: Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Authors: Wu, B. / Chien, E.Y. / Mol, C.D. / Fenalti, G. / Liu, W. / Katritch, V. / Abagyan, R. / Brooun, A. / Wells, P. / Bi, F.C. / Hamel, D.J. / Kuhn, P. / Handel, T.M. / Cherezov, V. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oe9.cif.gz | 351 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oe9.ent.gz | 298.3 KB | Display | PDB format |
PDBx/mmJSON format | 3oe9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/3oe9 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/3oe9 | HTTPS FTP |
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-Related structure data
Related structure data | 3oduC 3oe0C 3oe6C 3oe8C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56685.508 Da / Num. of mol.: 2 Fragment: CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Mutation: L125W, T240P, C1054T, C1097T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo Sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: CXCR4, CXCR4_HUMAN,E / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P61073, UniProt: P00720, lysozyme #2: Chemical | Sequence details | THE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 LYSOZYME INSERTED BETWEEN ...THE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 LYSOZYME INSERTED BETWEEN HIS228 AND GLY231 OF CXCR4, AS INDICATED AS CXCR4-3 IN THE PUBLICATIO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 9 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: Lipidic cubic phase made of monoolein and cholesterol, 27-35% PEG400, 0.27-0.33M Sodium malonate, 5mM Hexamine cobalt chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2010 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 24209 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 64.28 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.92 Å / Cor.coef. Fo:Fc: 0.8941 / Cor.coef. Fo:Fc free: 0.8834 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 105.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.821 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.24 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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