[English] 日本語
Yorodumi- PDB-4pjl: Myosin VI motor domain A458E mutant in the Pi release state, spac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pjl | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Myosin VI motor domain A458E mutant in the Pi release state, space group P212121 - | ||||||||||||
Components | Unconventional myosin-VI | ||||||||||||
Keywords | MOTOR PROTEIN / myosin VI / motor domain / Pi release state | ||||||||||||
Function / homology | Function and homology information myosin complex / clathrin-coated vesicle / microvillus / cytoskeletal motor activity / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / actin filament binding / Golgi apparatus / ATP binding Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Isabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
Funding support | France, United States, 3items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pjl.cif.gz | 326 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pjl.ent.gz | 258.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/4pjl ftp://data.pdbj.org/pub/pdb/validation_reports/pj/4pjl | HTTPS FTP |
---|
-Related structure data
Related structure data | 4pfoSC 4pfpC 4pjjC 4pjkC 4pjmC 4pjnC 4pk4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 89905.211 Da / Num. of mol.: 1 / Fragment: Residues 2-789 / Mutation: yes 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 | ||
---|---|---|---|
#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 7% PEG8k, 50mM Tris pH 7,5, 1mM TCEP, 10% Glycerol / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 53412 / % possible obs: 99.3 % / Redundancy: 4.82 % / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.34 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.84 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.28 / % possible all: 93.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PFO Resolution: 2.1→42 Å / Cor.coef. Fo:Fc: 0.9488 / Cor.coef. Fo:Fc free: 0.9319 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.151
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.29 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.217 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→42 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -1.2562 Å / Origin y: -4.104 Å / Origin z: 13.7451 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |