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Yorodumi- PDB-4pjn: Myosin VI motor domain in the Pi release state, space group P2121... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pjn | ||||||||||||
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Title | Myosin VI motor domain in the Pi release state, space group P212121 - shortly soaked with PO4 | ||||||||||||
Components | Unconventional myosin-VI | ||||||||||||
Keywords | MOTOR PROTEIN / Pi release state / myosin VI | ||||||||||||
Function / homology | Function and homology information inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / microvillus / endocytic vesicle / clathrin-coated pit / filopodium ...inner ear auditory receptor cell differentiation / vesicle transport along actin filament / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / microfilament motor activity / microvillus / endocytic vesicle / clathrin-coated pit / filopodium / actin filament organization / sensory perception of sound / ruffle membrane / endocytosis / actin filament binding / Golgi apparatus / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 4pjn.cif.gz | 325.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pjn.ent.gz | 257 KB | Display | PDB format |
PDBx/mmJSON format | 4pjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pjn_validation.pdf.gz | 788 KB | Display | wwPDB validaton report |
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Full document | 4pjn_full_validation.pdf.gz | 789.4 KB | Display | |
Data in XML | 4pjn_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 4pjn_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/4pjn ftp://data.pdbj.org/pub/pdb/validation_reports/pj/4pjn | HTTPS FTP |
-Related structure data
Related structure data | 4pfoC 4pfpC 4pjjC 4pjkC 4pjlC 4pjmC 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, 1 molecules A
#1: Protein | Mass: 89847.180 Da / Num. of mol.: 1 / 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, 561 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-ADP / | #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: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 7% PEG8K, 50mM Tris pH8,5, 1mM TCEP, 3% Glyc?rol, then soaked with 30% Glycerol and finaly soaked few secondes with 100mM NaH2PO4 pH 7.5 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2010 |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2→45 Å / Num. obs: 61572 / % possible obs: 99.4 % / Redundancy: 8.2 % / Biso Wilson estimate: 25.13 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.64 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.94 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.28 Å / Cor.coef. Fo:Fc: 0.9487 / Cor.coef. Fo:Fc free: 0.9328 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.136
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Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.221 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→29.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.1467 Å / Origin y: 3.9869 Å / Origin z: 13.759 Å
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Refinement TLS group | Selection details: { A|* } |