+Open data
-Basic information
Entry | Database: PDB / ID: 3j8i | ||||||
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Title | Near-Atomic Resolution for One State of F-Actin | ||||||
Components | Actin, alpha skeletal muscle | ||||||
Keywords | STRUCTURAL PROTEIN / helical polymer / F-actin | ||||||
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: 4.7 Å | ||||||
Authors | Galkin, V.E. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Near-atomic resolution for one state of F-actin. Authors: Vitold E Galkin / Albina Orlova / Matthijn R Vos / Gunnar F Schröder / Edward H Egelman / Abstract: Actin functions as a helical polymer, F-actin, but attempts to build an atomic model for this filament have been hampered by the fact that the filament cannot be crystallized and by structural ...Actin functions as a helical polymer, F-actin, but attempts to build an atomic model for this filament have been hampered by the fact that the filament cannot be crystallized and by structural heterogeneity. We have used a direct electron detector, cryo-electron microscopy, and the forces imposed on actin filaments in thin films to reconstruct one state of the filament at 4.7 Å resolution, which allows for building a reliable pseudo-atomic model of F-actin. We also report a different state of the filament where actin protomers adopt a conformation observed in the crystal structure of the G-actin-profilin complex with an open ATP-binding cleft. Comparison of the two structural states provides insights into ATP-hydrolysis and filament dynamics. The atomic model provides a framework for understanding why every buried residue in actin has been under intense selective pressure. | ||||||
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 | 3j8i.cif.gz | 335.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j8i.ent.gz | 278 KB | Display | PDB format |
PDBx/mmJSON format | 3j8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j8i_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3j8i_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3j8i_validation.xml.gz | 81 KB | Display | |
Data in CIF | 3j8i_validation.cif.gz | 115.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8i ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8i | HTTPS FTP |
-Related structure data
Related structure data | 6179MC 6180C 6181C 3j8jC 3j8kC 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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1 |
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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: -166.7 °) |
Details | Actin forms a helical filament of indeterminate length. The designation "pentameric" in REMARK 350 is an artifact of the PDB format and can be disregarded. |
-Components
#1: Protein | Mass: 42096.953 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-MG / |
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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: Skeletal muscle actin / Type: COMPLEX / Details: polymer |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 9, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 850 |
-Processing
EM software |
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Helical symmerty | Angular rotation/subunit: 166.7 ° / Axial rise/subunit: 27.6 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC / Nominal pixel size: 1.05 Å / Actual pixel size: 1.05 Å / Details: (Helical Details: IHRSR) / Symmetry type: HELICAL | ||||||||||||
Refinement step | Cycle: LAST
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