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Yorodumi- PDB-3mfp: Atomic model of F-actin based on a 6.6 angstrom resolution cryoEM map -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mfp | ||||||
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Title | Atomic model of F-actin based on a 6.6 angstrom resolution cryoEM map | ||||||
Components | Actin, alpha skeletal muscle | ||||||
Keywords | CONTRACTILE PROTEIN / helical filament / muscle protein | ||||||
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 / striated muscle thin filament ...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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.6 Å | ||||||
Authors | Fujii, T. / Iwane, A.H. / Yanagida, T. / Namba, K. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Authors: Takashi Fujii / Atsuko H Iwane / Toshio Yanagida / Keiichi Namba / Abstract: F-actin is a helical assembly of actin, which is a component of muscle fibres essential for contraction and has a crucial role in numerous cellular processes, such as the formation of lamellipodia ...F-actin is a helical assembly of actin, which is a component of muscle fibres essential for contraction and has a crucial role in numerous cellular processes, such as the formation of lamellipodia and filopodia, as the most abundant component and regulator of cytoskeletons by dynamic assembly and disassembly (from G-actin to F-actin and vice versa). Actin is a ubiquitous protein and is involved in important biological functions, but the definitive high-resolution structure of F-actin remains unknown. Although a recent atomic model well reproduced X-ray fibre diffraction intensity data from a highly oriented liquid-crystalline sol specimen, its refinement without experimental phase information has certain limitations. Direct visualization of the structure by electron cryomicroscopy, however, has been difficult because it is relatively thin and flexible. Here we report the F-actin structure at 6.6 Å resolution, made obtainable by recent advances in electron cryomicroscopy. The density map clearly resolves all the secondary structures of G-actin, such as α-helices, β-structures and loops, and makes unambiguous modelling and refinement possible. Complex domain motions that open the nucleotide-binding pocket on F-actin formation, specific D-loop and terminal conformations, and relatively tight axial but markedly loose interprotofilament interactions hydrophilic in nature are revealed in the F-actin model, and all seem to be important for dynamic functions of 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 | 3mfp.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mfp.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mfp_validation.pdf.gz | 823.8 KB | Display | wwPDB validaton report |
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Full document | 3mfp_full_validation.pdf.gz | 850.1 KB | Display | |
Data in XML | 3mfp_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3mfp_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/3mfp ftp://data.pdbj.org/pub/pdb/validation_reports/mf/3mfp | HTTPS FTP |
-Related structure data
Related structure data | 5168MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 27.6 Å / Rotation per n subunits: -166.656 °) |
-Components
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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#2: Chemical | ChemComp-ADP / |
-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: F-actin / Type: COMPLEX |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC / Date: Mar 21, 2009 |
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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: 100000 X / Calibrated magnification: 172414 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 1.6 mm |
Specimen holder | Temperature: 50 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Details: 16 mega pixels slow-scan CCD camera |
-Processing
EM software |
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3D reconstruction | Resolution: 6.6 Å / Actual pixel size: 1.742 Å / Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: REFINEMENT PROTOCOL--flexible fitting | ||||||||||||
Atomic model building | PDB-ID: 1J6Z | ||||||||||||
Refinement step | Cycle: LAST
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