+Open data
-Basic information
Entry | Database: PDB / ID: 5yu8 | ||||||||||||
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Title | Cofilin decorated actin filament | ||||||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Actin / Cofilin / muscle / cytoskeleton | ||||||||||||
Function / homology | Function and homology information actin filament fragmentation / Striated Muscle Contraction / actin filament severing / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix ...actin filament fragmentation / Striated Muscle Contraction / actin filament severing / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Tanaka, K. / Narita, A. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for cofilin binding and actin filament disassembly. Authors: Kotaro Tanaka / Shuichi Takeda / Kaoru Mitsuoka / Toshiro Oda / Chieko Kimura-Sakiyama / Yuichiro Maéda / Akihiro Narita / Abstract: Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin ...Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin (cofilin-decorated actin filament). The actin subunit structure of cofilactin (C-form) is distinct from those of F-actin (F-form) and monomeric actin (G-form). During the transition between these three conformations, the inner domain of actin (subdomains 3 and 4) and the majority of subdomain 1 move as two separate rigid bodies. The cofilin-actin interface consists of three distinct parts. Based on the rigid body movements of actin and the three cofilin-actin interfaces, we propose models for the cooperative binding of cofilin to actin, preferential binding of cofilin to ADP-bound actin filaments and cofilin-mediated severing of actin filaments. | ||||||||||||
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 | 5yu8.cif.gz | 389.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yu8.ent.gz | 310.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yu8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5yu8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5yu8_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 5yu8_validation.cif.gz | 89.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yu8 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yu8 | HTTPS FTP |
-Related structure data
Related structure data | 6844MC 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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-Components
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ACTA1, ACTA / Production host: Gallus gallus (chicken) / References: UniProt: P68139 #2: Protein | Mass: 18690.598 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CFL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P21566 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ADP / |
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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: Cofilin-decorated actin filament / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Gallus gallus (chicken) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: MOLYBDENUM / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 298 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 24 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Helical symmerty | Angular rotation/subunit: -162.1 ° / Axial rise/subunit: 27.6 Å / Axial symmetry: C1 | ||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86388 / Symmetry type: HELICAL |