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Yorodumi- PDB-4a7n: Structure of bare F-actin filaments obtained from the same sample... -
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-Basic information
Entry | Database: PDB / ID: 4a7n | ||||||
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Title | Structure of bare F-actin filaments obtained from the same sample as the Actin-Tropomyosin-Myosin Complex | ||||||
Components | F-ACTIN | ||||||
Keywords | STRUCTURAL PROTEIN / CYTOSKELETON / MYOSIN BINDING / ACTIN BINDING | ||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / 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 / single particle reconstruction / cryo EM / Resolution: 8.9 Å | ||||||
Authors | Behrmann, E. / Mueller, M. / Penczek, P.A. / Mannherz, H.G. / Manstein, D.J. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 4a7n.cif.gz | 314.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a7n.ent.gz | 260.8 KB | Display | PDB format |
PDBx/mmJSON format | 4a7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a7n_validation.pdf.gz | 1001.3 KB | Display | wwPDB validaton report |
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Full document | 4a7n_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4a7n_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 4a7n_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/4a7n ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a7n | HTTPS FTP |
-Related structure data
Related structure data | 1990MC 1987C 1988C 1989C 4a7fC 4a7hC 4a7lC 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: 41875.633 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE / References: UniProt: P68135 #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-CA / |
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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
Component | Name: BARE F-ACTIN FILAMENTS / Type: COMPLEX / Details: CMOS IMAGE FRAME SELECTED BY POWER SPECTRUM |
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Buffer solution | Name: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININE pH: 7.2 Details: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININE |
Specimen | Conc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS, |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC Details: BEST 836 MICROGRAPHS WERE SELECTED FROM OVER 3000 AQUIRED IMAGES |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 169644 X / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Cs: 4.1 mm |
Specimen holder | Temperature: 77 K |
Image recording | Electron dose: 17 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) |
Image scans | Num. digital images: 836 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||
3D reconstruction | Method: IHRSR / Resolution: 8.9 Å / Num. of particles: 4626 / Nominal pixel size: 1.84 Å / Actual pixel size: 1.84 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1990.(DEPOSITION ID: 10381). Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: METHOD--GEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH REFINEMENT PROTOCOL--EM | ||||||||||||
Atomic model building | PDB-ID: 3MFP | ||||||||||||
Refinement | Highest resolution: 8.9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.9 Å
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