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Yorodumi- PDB-4pfp: Myosin VI motor domain in the Pi release state (with Pi) space gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pfp | ||||||||||||
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Title | Myosin VI motor domain in the Pi release state (with Pi) space group P21 | ||||||||||||
Components | Unconventional myosin-VI | ||||||||||||
Keywords | MOTOR PROTEIN / Pi release state / Motor domain | ||||||||||||
Function / homology | Function and homology information myosin complex / clathrin-coated vesicle / cytoskeletal motor activity / microvillus / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / actin filament binding / Golgi apparatus ...myosin complex / clathrin-coated vesicle / cytoskeletal motor activity / microvillus / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / actin filament binding / Golgi apparatus / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.32 Å | ||||||||||||
Authors | Isabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
Funding support | France, United States, 3items
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Citation | Journal: Dev.Cell / Year: 2015 Title: How actin initiates the motor activity of Myosin. Authors: Llinas, P. / Isabet, T. / Song, L. / Ropars, V. / Zong, B. / Benisty, H. / Sirigu, S. / Morris, C. / Kikuti, C. / Safer, D. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pfp.cif.gz | 623.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pfp.ent.gz | 507.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pfp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4pfp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4pfp_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 4pfp_validation.cif.gz | 79.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/4pfp ftp://data.pdbj.org/pub/pdb/validation_reports/pf/4pfp | HTTPS FTP |
-Related structure data
Related structure data | 4pfoC 4pjjC 4pjkC 4pjlC 4pjmC 4pjnC 4pk4C 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
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 89847.180 Da / Num. of mol.: 2 / Fragment: Residues 2-789 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7 |
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-Non-polymers , 5 types, 419 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 4,5% PEG8k, 50mM MES pH 6,5, 1mM TCEP, 10mM NaH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2011 |
Radiation | Monochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→45 Å / Num. obs: 78052 / % possible obs: 99.8 % / Redundancy: 6.67 % / Biso Wilson estimate: 50.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 2.32→2.38 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.27 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Resolution: 2.32→23.39 Å / Cor.coef. Fo:Fc: 0.9496 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.212
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Displacement parameters | Biso mean: 54.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.32→23.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.38 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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