+Open data
-Basic information
Entry | Database: PDB / ID: 2d1k | |||||||||
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Title | Ternary complex of the WH2 domain of mim with actin-dnase I | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / WASP / WIP / WH2 / ACTIN / DNASE I | |||||||||
Function / homology | Function and homology information nephron tubule epithelial cell differentiation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / renal tubule morphogenesis / deoxyribonuclease I / plasma membrane organization / neutrophil activation involved in immune response ...nephron tubule epithelial cell differentiation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / renal tubule morphogenesis / deoxyribonuclease I / plasma membrane organization / neutrophil activation involved in immune response / deoxyribonuclease I activity / microspike assembly / cellular response to fluid shear stress / 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 / endocytic vesicle / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / cell surface receptor protein tyrosine kinase signaling pathway / ruffle / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear envelope / negative regulation of epithelial cell proliferation / calcium-dependent protein binding / actin cytoskeleton / lamellipodium / actin binding / cell body / actin cytoskeleton organization / cell adhesion / hydrolase activity / protein domain specific binding / signaling receptor 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 Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Chereau, D. / Kerff, F. / Dominguez, R. | |||||||||
Citation | Journal: Structure / Year: 2007 Title: Structural basis for the actin-binding function of missing-in-metastasis Authors: Lee, S.H. / Kerff, F. / Chereau, D. / Ferron, F. / Klug, A. / Dominguez, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d1k.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d1k.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 2d1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d1k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2d1k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2d1k_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 2d1k_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d1k ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d1k | HTTPS FTP |
-Related structure data
Related structure data | 2d1lC 2a41S S: Starting model for refinement 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135 |
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#2: Protein | Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P00639, deoxyribonuclease I |
-Protein/peptide / Sugars , 2 types, 2 molecules C
#3: Protein/peptide | Mass: 3611.075 Da / Num. of mol.: 1 / Fragment: WH2 Domain (residues 724-755) / Source method: obtained synthetically Details: synthetic peptide. This sequence occurs naturally in homo sapiens (humans) References: UniProt: O43312 |
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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 , 4 types, 107 molecules
#5: Chemical | #6: Chemical | ChemComp-ATP / | #7: Chemical | ChemComp-MG / | #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: 2.43 Å3/Da / Density % sol: 48.9 % |
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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: 14-BM-C / 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: 2.5→41.4 Å / Num. all: 23598 / Num. obs: 23598 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2069 / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2a41 Resolution: 2.5→41.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 26.973 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.383 / ESU R Free: 0.367 / 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: 58.805 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→41.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 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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