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- EMDB-1674: The cryo-EM structure of actin filament in the presence of phosphate -

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Basic information

Entry
Database: EMDB / ID: EMD-1674
TitleThe cryo-EM structure of actin filament in the presence of phosphate
Map dataThis is an image of a surface with B-factor correction.
Sample
  • Sample: Actin filament in the presence of phosphate
  • Protein or peptide: Actin
Keywordsactin / cytoskeleton / cell adhesion / cellular signaling / cytokinesis / muscle
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 / stress fiber / skeletal muscle fiber development / 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
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsMurakami K / Yasunaga T / Noguchi TQ / Uyeda TQ / Wakabayashi T
CitationJournal: Cell / Year: 2010
Title: Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
Authors: Kenji Murakami / Takuo Yasunaga / Taro Q P Noguchi / Yuki Gomibuchi / Kien X Ngo / Taro Q P Uyeda / Takeyuki Wakabayashi /
Abstract: Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. ...Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. Here, we present the cryo-electron microscopic (cryo-EM) structure of filamentous actin (F-actin) in the presence of phosphate, with the visualization of some α-helical backbones and large side chains. A complete atomic model based on the EM map identified intermolecular interactions mediated by bound magnesium and phosphate ions. Comparison of the F-actin model with G-actin monomer crystal structures reveals a critical role for bending of the conserved proline-rich loop in triggering phosphate release following ATP hydrolysis. Crystal structures of G-actin show that mutations in this loop trap the catalytic site in two intermediate states of the ATPase cycle. The combined structural information allows us to propose a detailed molecular mechanism for the biochemical events, including actin polymerization and ATPase activation, critical for actin filament dynamics.
History
DepositionJan 6, 2010-
Header (metadata) releaseJun 16, 2010-
Map releaseOct 19, 2010-
UpdateDec 23, 2011-
Current statusDec 23, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 40
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 40
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3g37
  • Surface level: 40
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3g37
  • Surface level: 35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1674.png

Downloads & links

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Map

FileDownload / File: emd_1674.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface with B-factor correction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.28 Å/pix.
x 121 pix.
= 275.275 Å		2.28 Å/pix.
x 121 pix.
= 275.275 Å		2.28 Å/pix.
x 121 pix.
= 275.275 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.275 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 33.0 / Movie #1: 40
Minimum - Maximum-66.216200000000001 - 105.405000000000001
Average (Standard dev.)0.454097 (±12.051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions121121121
Spacing121121121
CellA=B=C: 275.275 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2752.2752.275
M x/y/z121121121
origin x/y/z0.0000.0000.000
length x/y/z275.275275.275275.275
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS121121121
D min/max/mean-66.216105.4050.454

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Supplemental data

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Sample components

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Entire : Actin filament in the presence of phosphate

EntireName: Actin filament in the presence of phosphate
Components
  • Sample: Actin filament in the presence of phosphate
  • Protein or peptide: Actin

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Supramolecule #1000: Actin filament in the presence of phosphate

SupramoleculeName: Actin filament in the presence of phosphate / type: sample / ID: 1000 / Oligomeric state: Filament / Number unique components: 1
Molecular weightTheoretical: 1.17 MDa

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Macromolecule #1: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 1 / Name.synonym: Actin / Number of copies: 26 / Oligomeric state: Filament / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Muscle
Molecular weightTheoretical: 45 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 50 mM NaCl, 5 mM MgCl2, 0.025 mM ATP, 10 mM sodium phosphate (pH 7.4), 0.05 %NaN3, and 0.7 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 77 K / Instrument: OTHER

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Electron microscopy

MicroscopeHITACHI EF2000
TemperatureMin: 77 K / Max: 77 K / Average: 77 K
Specialist opticsEnergy filter - Name: HITACH
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 2.275 µm / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EOS / Number images used: 8000
Final two d classificationNumber classes: 72

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Atomic model buiding 1

SoftwareName: O, NAMD, EOS
DetailsProtocol: Real-space refinement. The initial model was docked manually and refined using O, NAMD, and EOS.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor
Output model

PDB-3g37:
Cryo-EM structure of actin filament in the presence of phosphate

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