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Yorodumi- PDB-4anj: MYOSIN VI (MDinsert2-GFP fusion) PRE-POWERSTROKE STATE (MG.ADP.AlF4) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4anj | ||||||
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Title | MYOSIN VI (MDinsert2-GFP fusion) PRE-POWERSTROKE STATE (MG.ADP.AlF4) | ||||||
Components |
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Keywords | MOTOR PROTEIN/METAL-BINDNG PROTEIN / MOTOR PROTEIN-METAL-BINDNG PROTEIN COMPLEX / MOLECULAR MOTOR / METAL-BINDING PROTEIN / TRANSITION STATE / PRE-POWERSTROKE STATE / GFP FUSION | ||||||
Function / homology | Function and homology information negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex ...negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex / regulation of secretion / kinetochore organization / autophagic cell death / : / G protein-coupled opsin signaling pathway / actin filament-based movement / inner ear auditory receptor cell differentiation / myosin V binding / vesicle transport along actin filament / channel regulator activity / cellular response to ethanol / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / muscle cell cellular homeostasis / microfilament motor activity / mitotic spindle pole / myosin heavy chain binding / cytoskeletal motor activity / filamentous actin / centriole replication / microvillus / DNA damage response, signal transduction by p53 class mediator / endocytic vesicle / enzyme regulator activity / ruffle / centriole / bioluminescence / filopodium / generation of precursor metabolites and energy / actin filament / actin filament organization / sensory perception of sound / intracellular protein transport / protein localization / mitotic spindle / ADP binding / ruffle membrane / spindle / endocytosis / actin filament binding / sensory perception of smell / actin cytoskeleton / cell cortex / midbody / cytoplasmic vesicle / nuclear membrane / calmodulin binding / protein phosphorylation / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) AEQUOREA VICTORIA (jellyfish) DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Menetrey, J. / Isabet, T. / Ropars, V. / Mukherjea, M. / Pylypenko, O. / Liu, X. / Perez, J. / Vachette, P. / Sweeney, H.L. / Houdusse, A.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2012 Title: Processive Steps in the Reverse Direction Require Uncoupling of the Lead Head Lever Arm of Myosin Vi. Authors: Menetrey, J. / Isabet, T. / Ropars, V. / Mukherjea, M. / Pylypenko, O. / Liu, X. / Perez, J. / Vachette, P. / Sweeney, H.L. / Houdusse, A.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4anj.cif.gz | 238.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4anj.ent.gz | 184 KB | Display | PDB format |
PDBx/mmJSON format | 4anj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4anj_validation.pdf.gz | 797.6 KB | Display | wwPDB validaton report |
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Full document | 4anj_full_validation.pdf.gz | 808.5 KB | Display | |
Data in XML | 4anj_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 4anj_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/4anj ftp://data.pdbj.org/pub/pdb/validation_reports/an/4anj | HTTPS FTP |
-Related structure data
Related structure data | 4e7sC 4e7zC 2v26S 3dqaS S: Starting model for refinement 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 120131.617 Da / Num. of mol.: 1 / Fragment: MYOSIN-6 RESIDUES 1-817, GFP RESIDUES 2-238 Source method: isolated from a genetically manipulated source Details: CHIMERIC PROTEIN, MYOSIN-6 RESIDUES 1-816 (AUTHOR NUMBERING) AND COMPLETE GFP (AFTER INITIATION METHIONINE REMOVAL) Source: (gene. exp.) SUS SCROFA (pig), (gene. exp.) AEQUOREA VICTORIA (jellyfish) Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122, UniProt: P42212 |
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#2: Protein | Mass: 16825.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152 |
-Non-polymers , 5 types, 97 molecules
#3: Chemical | ChemComp-ADP / | ||
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#4: Chemical | ChemComp-MG / | ||
#5: Chemical | ChemComp-ALF / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | GFP FUSED TO MYOSIN VI, THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI ...GFP FUSED TO MYOSIN VI, THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY INCORRECT BECAUSE THE CHANGES THAT ARE IN THEIR CLONE (LYS DELETION AND THE 6 MUTATIONS) ARE CONSERVED ACROSS THE MYOSIN VI FAMILY. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % / Description: NONE |
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Crystal grow | Details: 5% PEG 8000, 50 MM MES PH 5.5, 100 MM NH4SO4, 20 MM MGCL2, 20 MM NACL AND 3 % PROPAN-2-OL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.8 Å / Num. obs: 51178 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.6→48.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2V26, 3DQA Resolution: 2.6→137.36 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.84 / SU B: 11.08 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SIDE-CHAINS. THAT HAVE NO DEFINED ELECTRON DENSITY WERE OMITTED FROM THE MODEL. REGIONS 35-38, 175-177, 355-361, 395-407 AND 623-638, FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SIDE-CHAINS. THAT HAVE NO DEFINED ELECTRON DENSITY WERE OMITTED FROM THE MODEL. REGIONS 35-38, 175-177, 355-361, 395-407 AND 623-638, FROM THE MYOSIN VI (CHAIN A) AND REGIONS 27-30, 76- 79 AND 111- 116 FROM THE CALMODULIN (CHAIN B) HAVE NO DEFINED ELECTRON DENSITY AND WERE OMITTED FROM THE MODEL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.874 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→137.36 Å
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Refine LS restraints |
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