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Open data
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Basic information
Entry | Database: PDB / ID: 5oof | |||||||||||||||
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Title | Cryo-EM structure of F-actin in complex with ADP-BeFx | |||||||||||||||
![]() | Actin, alpha skeletal muscle![]() | |||||||||||||||
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Function / homology | ![]() cytoskeletal motor activator activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Merino, F. / Pospich, S. / Funk, J. / Kuellmer, F. / Arndt, H.-D. / Bieling, P. / Raunser, S. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM. Authors: Felipe Merino / Sabrina Pospich / Johanna Funk / Thorsten Wagner / Florian Küllmer / Hans-Dieter Arndt / Peter Bieling / Stefan Raunser / ![]() Abstract: The function of actin is coupled to the nucleotide bound to its active site. ATP hydrolysis is activated during polymerization; a delay between hydrolysis and inorganic phosphate (P) release results ...The function of actin is coupled to the nucleotide bound to its active site. ATP hydrolysis is activated during polymerization; a delay between hydrolysis and inorganic phosphate (P) release results in a gradient of ATP, ADP-P and ADP along actin filaments (F-actin). Actin-binding proteins can recognize F-actin's nucleotide state, using it as a local 'age' tag. The underlying mechanism is complex and poorly understood. Here we report six high-resolution cryo-EM structures of F-actin from rabbit skeletal muscle in different nucleotide states. The structures reveal that actin polymerization repositions the proposed catalytic base, His161, closer to the γ-phosphate. Nucleotide hydrolysis and P release modulate the conformational ensemble at the periphery of the filament, thus resulting in open and closed states, which can be sensed by coronin-1B. The drug-like toxin jasplakinolide locks F-actin in an open state. Our results demonstrate in detail how ATP hydrolysis links to F-actin's conformational dynamics and protein interaction. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 355.8 KB | Display | ![]() |
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PDB format | ![]() | 299.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3839MC ![]() 3835C ![]() 3836C ![]() 3837C ![]() 3838C ![]() 4259C ![]() 5onvC ![]() 5oocC ![]() 5oodC ![]() 5ooeC ![]() 6fhlC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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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 natural source / Source: (natural) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ADP / ![]() #3: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: ![]() |
Crystal symmetry | ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name H-M: P1 |
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Sample preparation
Component | Name: Filamentous alpha actin in complex with ADP-BeFx / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 5 mM HEPES pH 7.5, 0.1 M KCl, 2 mM MgCl2, 2 mM, 2 mM NaN3, 1 mM TCEP, 0.2 mM ADP, 0.2 mM BeF2 and 5 mM NaF. | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K Details: Manual backside blotting using Whatman filter paper No.5. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: Cs-corrected microscope |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 83 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2002 |
EM imaging optics | Spherical aberration corrector![]() |
Image scans | Movie frames/image: 25 / Used frames/image: 1-5 |
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Processing
EM software |
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Crystal symmetry | ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name H-M: P1 | ||||||||||||||||||||||||||||||||||||||||
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 366327 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 341850 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Rosetta iterative refinement was combined with MDFF. |