[English] 日本語
Yorodumi- PDB-3mmv: Structures of actin-bound WH2 domains of Spire and the implicatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mmv | ||||||
---|---|---|---|---|---|---|---|
Title | Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation | ||||||
Components |
| ||||||
Keywords | Contractile Protein/Protein binding / Spire / WH2 domain / 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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle ...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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / MAP2K and MAPK activation / oocyte karyosome formation / Platelet degranulation / RHO GTPases Activate WASPs and WAVEs / establishment of meiotic spindle localization / Regulation of actin dynamics for phagocytic cup formation / actin filament-based process / pole plasm oskar mRNA localization / DNA Damage Recognition in GG-NER / pole plasm assembly / Clathrin-mediated endocytosis / polar body extrusion after meiotic divisions / sperm individualization / actin filament network formation / UCH proteinases / actin nucleation / Golgi vesicle transport / brahma complex / maintenance of protein location in cell / cleavage furrow formation / Ino80 complex / tube formation / RSC-type complex / SWI/SNF 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 / regulation of transcription by RNA polymerase II / 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: 2.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mmv.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mmv.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mmv_validation.pdf.gz | 768.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3mmv_full_validation.pdf.gz | 776.9 KB | Display | |
Data in XML | 3mmv_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3mmv_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/3mmv ftp://data.pdbj.org/pub/pdb/validation_reports/mm/3mmv | HTTPS FTP |
-Related structure data
Related structure data | 3mn5C 3mn6C 3mn7C 3mn9C 2hf4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Protein/peptide | Mass: 1635.006 Da / Num. of mol.: 1 / Fragment: UNP residues 428-485, 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 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ATP / |
#5: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF CHAIN X IS : KKDAHAMILE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Ammonium sulphate 0.1 M MES pH 6.5 20%PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9801 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 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: 2.6→50 Å / Num. all: 15739 / Num. obs: 11584 / % possible obs: 73.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.6→2.8 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.4 / % possible all: 40.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HF4 Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.794 / SU B: 20.134 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 50.969 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
|