+Open data
-Basic information
Entry | Database: PDB / ID: 2p9l | ||||||
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Title | Crystal Structure of bovine Arp2/3 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / actin / WD repeat / complex | ||||||
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 / cilium assembly / positive regulation of double-strand break repair via homologous recombination ...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 / cilium assembly / positive regulation of double-strand break repair via homologous recombination / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Nolen, B.J. / Pollard, T.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Insights into the Influence of Nucleotides on Actin Family Proteins from Seven Structures of Arp2/3 Complex. Authors: Nolen, B.J. / 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 | 2p9l.cif.gz | 348 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p9l.ent.gz | 275.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p9l_validation.pdf.gz | 495.2 KB | Display | wwPDB validaton report |
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Full document | 2p9l_full_validation.pdf.gz | 551.9 KB | Display | |
Data in XML | 2p9l_validation.xml.gz | 63.7 KB | Display | |
Data in CIF | 2p9l_validation.cif.gz | 86.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/2p9l ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p9l | HTTPS FTP |
-Related structure data
Related structure data | 2p9iC 2p9kC 2p9nC 2p9pC 2p9sC 2p9uC C: citing same article (ref.) |
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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-like protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 47428.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ACTR3 / References: UniProt: P61157 |
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#2: Protein | Mass: 44818.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ACTR2 / References: UniProt: A7MB62 |
-Actin-related protein 2/3 complex subunit ... , 5 types, 5 molecules CDEFG
#3: Protein | Mass: 41016.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARPC1B / References: UniProt: Q58CQ2 |
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#4: Protein | Mass: 34402.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARPC2 / References: UniProt: Q3MHR7 |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARPC3 / References: UniProt: Q3T035 |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARPC4 / References: UniProt: Q148J6 |
#7: Protein | Mass: 16295.317 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARPC5 / References: UniProt: Q3SYX9 |
-Non-polymers , 1 types, 123 molecules
#8: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 7.5% PEG3350 50mM HEPES 100mM KSCN 10% Sucrose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 85537 / Num. obs: 81688 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.117 / Χ2: 1.107 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.97 / Num. unique all: 7556 / Χ2: 0.918 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 44.501 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.221 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→30 Å
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Refine LS restraints |
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Xplor file |
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