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Yorodumi- PDB-3mn9: Structures of actin-bound WH2 domains of Spire and the implicatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mn9 | ||||||
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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 / Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / VEGFA-VEGFR2 Pathway / : / Cell-extracellular matrix interactions ...chorion-containing eggshell formation / pole plasm RNA localization / Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / VEGFA-VEGFR2 Pathway / : / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / establishment of meiotic spindle localization / MAP2K and MAPK activation / oocyte karyosome formation / Platelet degranulation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / actin filament-based process / pole plasm oskar mRNA localization / DNA Damage Recognition in GG-NER / UCH proteinases / pole plasm assembly / Clathrin-mediated endocytosis / polar body extrusion after meiotic divisions / sperm individualization / actin filament network formation / actin nucleation / Golgi vesicle transport / brahma complex / maintenance of protein location in cell / cleavage furrow formation / tube formation / Ino80 complex / oogenesis / regulation of cytoskeleton organization / mitotic cytokinesis / intracellular transport / vesicle-mediated transport / actin filament polymerization / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / protein transport / actin binding / cell cortex / actin cytoskeleton organization / microtubule binding / cytoskeleton / hydrolase activity / chromatin remodeling / perinuclear region of cytoplasm / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 3mn9.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mn9.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mn9 ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mn9 | HTTPS FTP |
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-Related structure data
Related structure data | 3mmvC 3mn5C 3mn6C 3mn7C 2hf4S 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
#1: Protein | Mass: 41723.527 Da / Num. of mol.: 1 / Mutation: A204E, P243K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10987 |
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#2: Protein/peptide | Mass: 1635.006 Da / Num. of mol.: 1 / Fragment: UNP residues 371-485 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 |
#3: Chemical | ChemComp-ATP / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF CHAIN X IS : VQVIDELRRG VRLKKSNHER TPIEYELTPY EILMGDIRAK KYQLRKVMVN GDIPPRVKKD ...THE SEQUENCE OF CHAIN X IS : VQVIDELRRG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.2M Ammonium formate pH 6.6 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: 0.9792 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2010 / 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: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 29535 / Num. obs: 22506 / % possible obs: 76.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2→2.3 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.9 / % possible all: 38.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HF4 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.951 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.229 / 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: 42.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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