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Yorodumi- PDB-3mn5: Structures of actin-bound WH2 domains of Spire and the implicatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mn5 | ||||||
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Title | Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation | ||||||
Components |
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Keywords | Contractile Protein/Protein binding / WH2 domain / Spire / Actin complex / Contractile Protein-Protein binding complex | ||||||
Function / homology | Function and homology information chorion-containing eggshell formation / pole plasm RNA localization / establishment of meiotic spindle localization / oocyte karyosome formation / actin filament-based process / pole plasm oskar mRNA localization / pole plasm assembly / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation ...chorion-containing eggshell formation / pole plasm RNA localization / establishment of meiotic spindle localization / oocyte karyosome formation / actin filament-based process / pole plasm oskar mRNA localization / pole plasm assembly / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / cytoskeletal motor activator activity / oogenesis / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / regulation of cytoskeleton organization / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / intracellular transport / skeletal muscle fiber development / stress fiber / vesicle-mediated transport / titin binding / actin filament polymerization / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / calcium-dependent protein binding / protein transport / lamellipodium / cell body / actin binding / cell cortex / actin cytoskeleton organization / microtubule binding / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ducka, A.M. / Sitar, T. / Popowicz, G.M. / Huber, R. / Holak, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation. Authors: Ducka, A.M. / Joel, P. / Popowicz, G.M. / Trybus, K.M. / Schleicher, M. / Noegel, A.A. / Huber, R. / Holak, T.A. / Sitar, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mn5.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mn5.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mn5 ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mn5 | HTTPS FTP |
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-Related structure data
Related structure data | 3mmvC 3mn6C 3mn7C 3mn9C 1nwkS 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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Details | complex of Actin and Spire |
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AS
#1: Protein | Mass: 40087.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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#2: Protein/peptide | Mass: 4311.981 Da / Num. of mol.: 1 / Fragment: UNP residues 448-485, WH2 2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spir, p150-Spir, CG10076 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U1K1 |
-Non-polymers , 4 types, 492 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-ATP / |
#5: Chemical | ChemComp-LAB / |
#6: 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: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.2 Magnesium formate pH 5.9 20% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9801 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2009 / Details: LN2 cooled fixed-exit Si(111) monochromator |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 62290 / Num. obs: 49209 / % possible obs: 79 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 1.5→1.6 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 4.4 / % possible all: 38.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NWK Resolution: 1.5→39.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.334 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.832 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→39.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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