+Open data
-Basic information
Entry | Database: PDB / ID: 6djn | |||||||||
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Title | Cryo-EM structure of ADP-Pi-actin filaments | |||||||||
Components | Actin, alpha skeletal muscle | |||||||||
Keywords | CONTRACTILE PROTEIN / actin / ADP-Pi / filament / ATPase | |||||||||
Function / homology | Function and homology information Striated Muscle Contraction / 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 / hydrolase activity / ATP binding Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Chou, S.Z. / Pollard, T.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides. Authors: Steven Z Chou / Thomas D Pollard / Abstract: We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound AMPPNP (β,γ-imidoadenosine 5'-triphosphate, an ATP analog, resolution 3.1 Å), ADP-P (ADP with inorganic ...We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound AMPPNP (β,γ-imidoadenosine 5'-triphosphate, an ATP analog, resolution 3.1 Å), ADP-P (ADP with inorganic phosphate, resolution 3.1 Å), or ADP (resolution 3.6 Å). Subunits in the three filaments have similar backbone conformations, so assembly rather than ATP hydrolysis or phosphate dissociation is responsible for their flattened conformation in filaments. Polymerization increases the rate of ATP hydrolysis by changing the positions of the side chains of Q137 and H161 in the active site. Flattening during assembly also promotes interactions along both the long-pitch and short-pitch helices. In particular, conformational changes in subdomain 3 open up multiple favorable interactions with the DNase-I binding loop in subdomain 2 of the adjacent subunit. Subunits at the barbed end of the filament are likely to be in this favorable conformation, while monomers are not. This difference explains why filaments grow faster at the barbed end than the pointed end. When phosphate dissociates from ADP-P-actin through a backdoor channel, the conformation of the C terminus changes so it distorts the DNase binding loop, which allows cofilin binding, and a network of interactions among S14, H73, G74, N111, R177, and G158 rearranges to open the phosphate release site. | |||||||||
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 | 6djn.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6djn.ent.gz | 217.3 KB | Display | PDB format |
PDBx/mmJSON format | 6djn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6djn_validation.pdf.gz | 892.2 KB | Display | wwPDB validaton report |
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Full document | 6djn_full_validation.pdf.gz | 902.9 KB | Display | |
Data in XML | 6djn_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 6djn_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/6djn ftp://data.pdbj.org/pub/pdb/validation_reports/dj/6djn | HTTPS FTP |
-Related structure data
Related structure data | 7937MC 7936C 7938C 6djmC 6djoC 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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-Components
#1: Protein | Mass: 41875.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-PO4 / |
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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: ADP-Pi-actin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Gallus gallus (chicken) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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 / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 43.54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -166.56 ° / Axial rise/subunit: 27.42 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 411164 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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