+Open data
-Basic information
Entry | Database: PDB / ID: 1y64 | ||||||
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Title | Bni1p Formin Homology 2 Domain complexed with ATP-actin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / FH2 ACTIN CYTOSKELETON / COILED COIL / ACTIN / TETRAMETHYLRHODAMINE-5-MALEIMIDE / ATP-STATE | ||||||
Function / homology | Function and homology information polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / mitotic actomyosin contractile ring assembly / vesicle targeting / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip ...polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / mitotic actomyosin contractile ring assembly / vesicle targeting / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip / profilin binding / cellular bud neck / mating projection tip / barbed-end actin filament capping / cellular hyperosmotic response / cytoskeletal motor activator activity / establishment of cell polarity / tropomyosin binding / mesenchyme migration / cell division site / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / establishment of mitotic spindle orientation / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / regulation of actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / calcium-dependent protein binding / regulation of protein localization / lamellipodium / actin binding / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å | ||||||
Authors | Otomo, T. / Tomchick, D.R. / Otomo, C. / Panchal, S.C. / Machius, M. / Rosen, M.K. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain Authors: Otomo, T. / Tomchick, D.R. / Otomo, C. / Panchal, S.C. / Machius, M. / Rosen, M.K. #1: Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Crystal Structures Of A Formin Homology-2 Domain Reveal A Tethered-Dimer Architecture Authors: Xu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J. #2: Journal: Mol.Cell / Year: 2004 Title: The Core FH2 Domain of Diaphanous-Related Formins Is an Elongated Actin Binding Protein that Inhibits Polymerization Authors: Shimada, A. / Nyitrai, M. / Vetter, I.R. / Kuhlmann, D. / Bugyi, B. / Narumiya, S. / Geeves, M.A. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y64.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y64.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 1y64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y64_validation.pdf.gz | 785.6 KB | Display | wwPDB validaton report |
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Full document | 1y64_full_validation.pdf.gz | 876 KB | Display | |
Data in XML | 1y64_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 1y64_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y64 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y64 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P68135 |
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#2: Protein | Mass: 50921.957 Da / Num. of mol.: 1 / Fragment: FH2 DOMAIN, RESIDUES 1327-1769 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BNI1, PPF3, SHE5 / Production host: Escherichia coli (E. coli) / References: UniProt: P41832 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ATP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: potassium bromide, hepes, DTT, Tris, ATP, calcium chloride, ethylene glycol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99987, 0.9797, 0.97981, 0.96411 | |||||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 20, 2004 | |||||||||||||||
Radiation | Monochromator: Silicon crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.05→31.78 Å / Num. all: 26458 / Num. obs: 26458 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 113 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.4 | |||||||||||||||
Reflection shell | Resolution: 3.05→3.08 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1314 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a free: 1.16 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→30 Å
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Refine LS restraints |
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