+Open data
-Basic information
Entry | Database: PDB / ID: 7pm3 | ||||||||||||||||||
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Title | Cryo-EM structure of young JASP-stabilized F-actin (central 3er) | ||||||||||||||||||
Components | Actin, alpha skeletal muscle | ||||||||||||||||||
Keywords | STRUCTURAL PROTEIN / myosin / cytoskeleton / F-actin / jasplakinolide | ||||||||||||||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Pospich, S. / Sweeney, H.L. / Houdusse, A. / Raunser, S. | ||||||||||||||||||
Funding support | Germany, European Union, France, United States, 5items
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Citation | Journal: Elife / Year: 2021 Title: High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. Authors: Sabrina Pospich / H Lee Sweeney / Anne Houdusse / Stefan Raunser / Abstract: The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding are ...The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding are only partially understood, mostly due to sparse structural data on actin-bound states of myosin. Here, we report 26 high-resolution cryo-EM structures of the actomyosin-V complex in the strong-ADP, rigor, and a previously unseen post-rigor transition state that binds the ATP analog AppNHp. The structures reveal a high flexibility of myosin in each state and provide valuable insights into the structural transitions of myosin-V upon ADP release and binding of AppNHp, as well as the actomyosin interface. In addition, they show how myosin is able to specifically alter the structure of F-actin. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7pm3.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pm3.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 7pm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/7pm3 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/7pm3 | HTTPS FTP |
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-Related structure data
Related structure data | 13511MC 7pltC 7pluC 7plvC 7plwC 7plxC 7plyC 7plzC 7pm0C 7pm1C 7pm2C 7pm5C 7pm6C 7pm7C 7pm8C 7pm9C 7pmaC 7pmbC 7pmcC 7pmdC 7pmeC 7pmfC 7pmgC 7pmhC 7pmiC 7pmjC 7pmlC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 42109.973 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Young JASP-stabilized F-actin / Type: COMPLEX Details: Young ADP-Pi-bound F-actin stabilized with jasplakinolide Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Rise 27.9 A, Twist -166.9 degrees |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 0 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 15 sec. / Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1064 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Spherical aberration corrector: Cs-corrected microscope |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212660 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: An initial model of jasplakinolide was generated using elBow within Phenix inputting the SMILES string. | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOD Pdb chain-ID: C | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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