+Open data
-Basic information
Entry | Database: PDB / ID: 2a40 | |||||||||
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Title | Ternary complex of the WH2 domain of WAVE with Actin-DNAse I | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / WAVE / WH2 / WASP / Actin / DNAse I / arp2/3 | |||||||||
Function / homology | Function and homology information SCAR complex / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / lamellipodium morphogenesis / ameboidal-type cell migration / positive regulation of Arp2/3 complex-mediated actin nucleation / deoxyribonuclease I / Arp2/3 complex binding / actin filament-based movement ...SCAR complex / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / lamellipodium morphogenesis / ameboidal-type cell migration / positive regulation of Arp2/3 complex-mediated actin nucleation / deoxyribonuclease I / Arp2/3 complex binding / actin filament-based movement / postsynaptic actin cytoskeleton organization / neutrophil activation involved in immune response / deoxyribonuclease I activity / DNA catabolic process / negative regulation of stress fiber assembly / lamellipodium assembly / protein kinase A binding / cytoskeletal motor activator activity / megakaryocyte development / Fc-gamma receptor signaling pathway involved in phagocytosis / tropomyosin binding / mesenchyme migration / Rac protein signal transduction / troponin I binding / myosin heavy chain binding / protein kinase A regulatory subunit binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / RHO GTPases Activate WASPs and WAVEs / vascular endothelial growth factor receptor signaling pathway / skeletal muscle fiber development / positive regulation of lamellipodium assembly / stress fiber / titin binding / ruffle / viral process / actin filament polymerization / filopodium / actin filament / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / SH3 domain binding / endocytosis / nuclear envelope / calcium-dependent protein binding / cell-cell junction / actin cytoskeleton / lamellipodium / actin binding / basolateral plasma membrane / cell body / actin cytoskeleton organization / angiogenesis / early endosome / cadherin binding / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / apoptotic process / magnesium ion binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Chereau, D. / Kerff, F. / Dominguez, R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly Authors: Chereau, D. / Kerff, F. / Graceffa, P. / Grabarek, Z. / Langsetmo, K. / Dominguez, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a40.cif.gz | 295 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a40.ent.gz | 234.3 KB | Display | PDB format |
PDBx/mmJSON format | 2a40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a40_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 2a40_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2a40_validation.xml.gz | 56.9 KB | Display | |
Data in CIF | 2a40_validation.cif.gz | 83.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/2a40 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/2a40 | HTTPS FTP |
-Related structure data
Related structure data | 2a3zC 2a41C 2a42C 1atnS 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | Mass: 29092.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00639, deoxyribonuclease I |
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-Protein/peptide / Sugars , 2 types, 4 molecules CF
#3: Protein/peptide | Mass: 3822.230 Da / Num. of mol.: 2 / Fragment: WH2 domain, residues 433-464 / Source method: obtained synthetically Details: This sequence occurs naturally in Homo sapiens (humans) References: GenBank: 26454860, UniProt: Q9Y6W5*PLUS #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 912 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | #7: Chemical | #8: Chemical | #9: 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: 2.4 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: sodium formate, PEG3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.51 Å / Num. all: 132595 / Num. obs: 106912 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4 / Num. unique all: 6309 / % possible all: 69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ATN Resolution: 1.8→47.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.497 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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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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