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Yorodumi- PDB-3dxk: Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dxk | ||||||
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Title | Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636 | ||||||
Components | (Actin-related protein ...) x 7 | ||||||
Keywords | STRUCTURAL PROTEIN / beta-propeller / Acetylation / Actin-binding / ATP-binding / Cell projection / Cytoplasm / Cytoskeleton / Nucleotide-binding / Phosphoprotein / WD repeat | ||||||
Function / homology | Function and homology information EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly ...EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of lamellipodium assembly / actin filament polymerization / cell projection / structural constituent of cytoskeleton / actin filament binding / cell migration / site of double-strand break / actin binding / cell cortex / neuron projection / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Nolen, B.J. / Tomasevic, N. / Russell, A. / Pierce, D.W. / Jia, Z. / Hartman, J. / Sakowicz, R. / Pollard, T.D. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Characterization of two classes of small molecule inhibitors of Arp2/3 complex Authors: Nolen, B.J. / Tomasevic, N. / Russell, A. / Pierce, D.W. / Jia, Z. / McCormick, C.D. / Hartman, J. / Sakowicz, R. / Pollard, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dxk.cif.gz | 349 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dxk.ent.gz | 277.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dxk_validation.pdf.gz | 791.6 KB | Display | wwPDB validaton report |
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Full document | 3dxk_full_validation.pdf.gz | 842.6 KB | Display | |
Data in XML | 3dxk_validation.xml.gz | 62.7 KB | Display | |
Data in CIF | 3dxk_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dxk ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dxk | HTTPS FTP |
-Related structure data
Related structure data | 3dxmC 1k8kS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Actin-related protein ... , 7 types, 7 molecules ABCDEFG
#1: Protein | Mass: 47428.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61157 |
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#2: Protein | Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A7MB62 |
#3: Protein | Mass: 41030.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q58CQ2 |
#4: Protein | Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHR7 |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T035 |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q148J6 |
#7: Protein | Mass: 16251.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYX9 |
-Non-polymers , 2 types, 43 molecules
#8: Chemical | ChemComp-N23 / |
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#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 8% PEG 8000, 50 mM HEPES, pH 7.5, 100 mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 25, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 80652 / Num. obs: 78877 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.066 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.568 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1K8K Resolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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