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Yorodumi- PDB-7udu: cryo-EM structure of the ADP state wild type myosin-15-F-actin co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7udu | ||||||||||||
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Title | cryo-EM structure of the ADP state wild type myosin-15-F-actin complex (symmetry expansion and re-centering) | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / myosin motor proteins / actin cytoskeleton / stereocilia / deafness | ||||||||||||
Function / homology | Function and homology information actin-based cell projection / stereocilium bundle / Striated Muscle Contraction / stereocilium / myosin complex / inner ear morphogenesis / microfilament motor activity / skeletal muscle thin filament assembly / striated muscle thin filament / response to light stimulus ...actin-based cell projection / stereocilium bundle / Striated Muscle Contraction / stereocilium / myosin complex / inner ear morphogenesis / microfilament motor activity / skeletal muscle thin filament assembly / striated muscle thin filament / response to light stimulus / skeletal muscle fiber development / stress fiber / locomotory behavior / actin filament / actin filament organization / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||||||||
Authors | Gong, R. / Reynolds, M.J. / Alushin, G.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia. Authors: Rui Gong / Fangfang Jiang / Zane G Moreland / Matthew J Reynolds / Santiago Espinosa de Los Reyes / Pinar Gurel / Arik Shams / James B Heidings / Michael R Bowl / Jonathan E Bird / Gregory M Alushin / Abstract: The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin ...The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin regulatory machinery to stereocilia tips, myosin-15 directly nucleates actin filament ("F-actin") assembly, which is disrupted by a progressive hearing loss mutation (p.D1647G, ""). Here, we present cryo-electron microscopy structures of myosin-15 bound to F-actin, providing a framework for interpreting the impacts of deafness mutations on motor activity and actin nucleation. Rigor myosin-15 evokes conformational changes in F-actin yet maintains flexibility in actin's D-loop, which mediates inter-subunit contacts, while the mutant locks the D-loop in a single conformation. Adenosine diphosphate-bound myosin-15 also locks the D-loop, which correspondingly blunts actin-polymerization stimulation. We propose myosin-15 enhances polymerization by bridging actin protomers, regulating nucleation efficiency by modulating actin's structural plasticity in a myosin nucleotide state-dependent manner. This tunable regulation of actin polymerization could be harnessed to precisely control stereocilium height. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7udu.cif.gz | 349.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7udu.ent.gz | 285.3 KB | Display | PDB format |
PDBx/mmJSON format | 7udu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7udu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7udu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7udu_validation.xml.gz | 78.1 KB | Display | |
Data in CIF | 7udu_validation.cif.gz | 112.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/7udu ftp://data.pdbj.org/pub/pdb/validation_reports/ud/7udu | HTTPS FTP |
-Related structure data
Related structure data | 26460MC 7r8vC 7r91C 7rb8C 7rb9C 7udtC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 41631.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139 #2: Protein | | Mass: 82393.773 Da / Num. of mol.: 1 / Fragment: motor domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo15a, Myo15 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9QZZ4 #3: Protein | | Mass: 16936.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) Production host: Insect cell expression vector pTIE1 (others) #4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 Details: 10 mM imidazole pH 7.0, 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.01% NaN3 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: the ADP state wild type myosin-15 bound to F-actin | ||||||||||||||||||||||||||||||
Specimen support | Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 375696 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189104 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6BNO | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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