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Yorodumi- EMDB-1990: Structure of bare F-actin filaments obtained from the same sample... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1990 | |||||||||
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Title | Structure of bare F-actin filaments obtained from the same sample as the Actin-Tropomyosin-Myosin Complex | |||||||||
Map data | undecorated F-actin filament | |||||||||
Sample |
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Keywords | Structural protein / cytoskeleton / myosin binding / actin binding | |||||||||
Function / homology | Function and homology information : / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly ...: / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle 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 | helical reconstruction / cryo EM / Resolution: 8.9 Å | |||||||||
Authors | Behrmann E / Mueller M / Penczek PA / Mannherz HG / Manstein DJ / Raunser S | |||||||||
Citation | Journal: Cell / Year: 2012 Title: Structure of the rigor actin-tropomyosin-myosin complex. Authors: Elmar Behrmann / Mirco Müller / Pawel A Penczek / Hans Georg Mannherz / Dietmar J Manstein / Stefan Raunser / Abstract: Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions ...Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1990.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-1990-v30.xml emd-1990.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_1990.png | 108.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1990 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1990 | HTTPS FTP |
-Validation report
Summary document | emd_1990_validation.pdf.gz | 180.2 KB | Display | EMDB validaton report |
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Full document | emd_1990_full_validation.pdf.gz | 179.3 KB | Display | |
Data in XML | emd_1990_validation.xml.gz | 4.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1990 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1990 | HTTPS FTP |
-Related structure data
Related structure data | 4a7nMC 1987C 1988C 1989C 4a7fC 4a7hC 4a7lC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1990.map.gz / Format: CCP4 / Size: 21 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | undecorated F-actin filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bare F-actin filaments
Entire | Name: Bare F-actin filaments |
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Components |
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-Supramolecule #1000: Bare F-actin filaments
Supramolecule | Name: Bare F-actin filaments / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: F-actin
Macromolecule | Name: F-actin / type: protein_or_peptide / ID: 1 / Name.synonym: actin filament / Number of copies: 14 / Oligomeric state: filament / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: skeletal muscle / Organelle: Sarcoplasm / Location in cell: Sarcoplasm |
Sequence | GO: GO: 0042643 / InterPro: Actin family |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.2 Details: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine |
Grid | Details: C-Flat CF-2/1-4C copper 400 mesh |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 101 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Vitrification instrument: Gatan Cryoplunge 3 / Method: Manual blotting for approximately 15 seconds |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 77 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification |
Specialist optics | Energy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 12.0 eV |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Digitization - Sampling interval: 15.6 µm / Number real images: 836 / Average electron dose: 17 e/Å2 Details: Over 3000 images were taken of which only the best 836 were used for processing Bits/pixel: 14 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 169644 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: cryogenic stage with side entry access / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
Details | Particles were selected by hand using e2helixboxer |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.6 Å Applied symmetry - Helical parameters - Δ&Phi: 166.5 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX |
CTF correction | Details: each particle |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: DireX |
Details | Protocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-4a7n: |