+Open data
-Basic information
Entry | Database: PDB / ID: 2a41 | |||||||||
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Title | Ternary complex of the WH2 Domain of WIP with Actin-DNAse I | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / WIP / WH2 / WASP / actin / DNAse I / arp2/3 | |||||||||
Function / homology | Function and homology information regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / actin filament-based movement / profilin binding / neutrophil activation involved in immune response / deoxyribonuclease I activity / response to other organism / actin polymerization or depolymerization ...regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / actin filament-based movement / profilin binding / neutrophil activation involved in immune response / deoxyribonuclease I activity / response to other organism / actin polymerization or depolymerization / DNA catabolic process / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / CDC42 GTPase cycle / skeletal muscle myofibril / actin monomer binding / RHO GTPases Activate WASPs and WAVEs / skeletal muscle fiber development / stress fiber / titin binding / protein folding chaperone / ruffle / RAC1 GTPase cycle / actin filament polymerization / filopodium / actin filament / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / nuclear envelope / calcium-dependent protein binding / actin cytoskeleton / lamellipodium / actin binding / cell body / cytoplasmic vesicle / protein-containing complex assembly / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / apoptotic process / magnesium ion binding / DNA binding / 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: 2.6 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 | 2a41.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a41.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 2a41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a41_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2a41_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2a41_validation.xml.gz | 28 KB | Display | |
Data in CIF | 2a41_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/2a41 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/2a41 | HTTPS FTP |
-Related structure data
Related structure data | 2a3zC 2a40C 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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#2: Protein | Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00639, deoxyribonuclease I |
-Protein/peptide / Sugars , 2 types, 2 molecules C
#3: Protein/peptide | Mass: 3474.984 Da / Num. of mol.: 1 / Fragment: first WH2 domain / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: O43516 |
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 213 molecules
#5: Chemical | #6: Chemical | ChemComp-ATP / | #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-FMT / | #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: 2.39 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium formate, PEG3350, pH 7.0, 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 / 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: 2.6→45.08 Å / Num. all: 22916 / Num. obs: 21267 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 5 / Num. unique all: 1891 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1atn Resolution: 2.6→45.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 19.53 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.311 / 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: 34.779 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→45.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.671 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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