+Open data
-Basic information
Entry | Database: PDB / ID: 4wyb | |||||||||
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Title | Structure of the Bud6 flank domain in complex with actin | |||||||||
Components |
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Keywords | CONTRACTILE PROTEIN/PROTEIN BINDING / nucleation promoting factor WH2 Domain / Formin / CONTRACTILE PROTEIN-PROTEIN BINDING complex | |||||||||
Function / homology | Function and homology information cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity ...cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / positive regulation of actin nucleation / cell tip / astral microtubule organization / incipient cellular bud site / cellular bud tip / cellular bud neck / mating projection tip / cellular hyperosmotic response / spindle pole body / cytoskeletal motor activator activity / establishment of cell polarity / 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 / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / enzyme activator activity / 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 / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Oryctolagus cuniculus (rabbit) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.493 Å | |||||||||
Authors | Eck, M.J. / Park, E. / Zheng, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2015 Title: Structure of a Bud6/Actin Complex Reveals a Novel WH2-like Actin Monomer Recruitment Motif. Authors: Park, E. / Graziano, B.R. / Zheng, W. / Garabedian, M. / Goode, B.L. / Eck, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wyb.cif.gz | 927.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wyb.ent.gz | 762.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wyb_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 4wyb_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 4wyb_validation.xml.gz | 176.6 KB | Display | |
Data in CIF | 4wyb_validation.cif.gz | 226.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/4wyb ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wyb | HTTPS FTP |
-Related structure data
Related structure data | 3mn7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42096.953 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: ATP, Ca / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | Mass: 10540.659 Da / Num. of mol.: 12 / Fragment: residues 699-788 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: BUD6, AIP3, YLR319C, L8543.5 / Plasmid: pET Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P41697 #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.493→45.418 Å / Num. obs: 97910 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MN7 Resolution: 3.493→45.418 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.493→45.418 Å
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Refine LS restraints |
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LS refinement shell |
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