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- PDB-4pfo: Myosin VI motor domain in the Pi release state, space group P212121 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pfo | ||||||||||||
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Title | Myosin VI motor domain in the Pi release state, space group P212121 | ||||||||||||
![]() | Unconventional myosin-VI | ||||||||||||
![]() | MOTOR PROTEIN / Myosin / motor domain / Pi Release state | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Isabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.5 KB | Display | ![]() |
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PDB format | ![]() | 258.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.9 KB | Display | ![]() |
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Full document | ![]() | 781.1 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pfpC ![]() 4pjjC ![]() 4pjkC ![]() 4pjlC ![]() 4pjmC ![]() 4pjnC ![]() 4pk4C ![]() 2v26S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#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.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 6,25% PEG 8K, 50mM Tris pH 8,5, 1mM TCEP and 3% Glycerol with microseeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2010 |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45 Å / Num. obs: 90603 / % possible obs: 99.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.38 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.42 / % possible all: 94.9 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2v26 Resolution: 1.75→17.64 Å / Cor.coef. Fo:Fc: 0.9657 / Cor.coef. Fo:Fc free: 0.9621 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
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Displacement parameters | Biso mean: 39.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.223 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→17.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -1.1582 Å / Origin y: -3.8551 Å / Origin z: 13.6567 Å
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Refinement TLS group | Selection details: { A|* } |