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- EMDB-5168: Direct visualization of secondary structures of F-actin by electr... -

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Basic information

Entry
Database: EMDB / ID: EMD-5168
TitleDirect visualization of secondary structures of F-actin by electron cryomicroscopy
Map dataCryoEM map of F-actin at 6.6 angstrom resolution
Sample
  • Sample: F-actinActin
  • Protein or peptide: F-actinActin
KeywordsF-actin
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament 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
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 speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsFujii T / Iwane AH / Yanagida T / Namba K
CitationJournal: Nature / Year: 2010
Title: Direct visualization of secondary structures of F-actin by electron cryomicroscopy.
Authors: Takashi Fujii / Atsuko H Iwane / Toshio Yanagida / Keiichi Namba /
Abstract: F-actin is a helical assembly of actin, which is a component of muscle fibres essential for contraction and has a crucial role in numerous cellular processes, such as the formation of lamellipodia ...F-actin is a helical assembly of actin, which is a component of muscle fibres essential for contraction and has a crucial role in numerous cellular processes, such as the formation of lamellipodia and filopodia, as the most abundant component and regulator of cytoskeletons by dynamic assembly and disassembly (from G-actin to F-actin and vice versa). Actin is a ubiquitous protein and is involved in important biological functions, but the definitive high-resolution structure of F-actin remains unknown. Although a recent atomic model well reproduced X-ray fibre diffraction intensity data from a highly oriented liquid-crystalline sol specimen, its refinement without experimental phase information has certain limitations. Direct visualization of the structure by electron cryomicroscopy, however, has been difficult because it is relatively thin and flexible. Here we report the F-actin structure at 6.6 Å resolution, made obtainable by recent advances in electron cryomicroscopy. The density map clearly resolves all the secondary structures of G-actin, such as α-helices, β-structures and loops, and makes unambiguous modelling and refinement possible. Complex domain motions that open the nucleotide-binding pocket on F-actin formation, specific D-loop and terminal conformations, and relatively tight axial but markedly loose interprotofilament interactions hydrophilic in nature are revealed in the F-actin model, and all seem to be important for dynamic functions of actin.
History
DepositionFeb 8, 2010-
Header (metadata) releaseAug 11, 2010-
Map releaseSep 17, 2010-
UpdateSep 6, 2011-
Current statusSep 6, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3mfp
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3mfp
  • Surface level: 10
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5168_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5168.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of F-actin at 6.6 angstrom resolution
Voxel sizeX=Y=Z: 1.742 Å
Density
Contour LevelBy AUTHOR: 10.0 / Movie #1: 10
Minimum - Maximum-32.003100000000003 - 41.873399999999997
Average (Standard dev.)0.461301 (±3.3917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 174.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7421.7421.742
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z174.200174.200174.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-32.00341.8730.461

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Supplemental data

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Sample components

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Entire : F-actin

EntireName: F-actinActin
Components
  • Sample: F-actinActin
  • Protein or peptide: F-actinActin

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Supramolecule #1000: F-actin

SupramoleculeName: F-actin / type: sample / ID: 1000 / Oligomeric state: helical structure / Number unique components: 7

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Macromolecule #1: F-actin

MacromoleculeName: F-actin / type: protein_or_peptide / ID: 1 / Name.synonym: F-actin / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others) / synonym: rabbit

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Details: 25 mM Hepes buffer (pH 7.5), 50 mM KCl, 1 mM MgCl2 and 1 mM ATP
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3.5 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 172000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000
Specialist opticsEnergy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
Sample stageSpecimen holder: Top entry liquid helium-cooled cryo specimen holder
Specimen holder model: JEOL 3200FSC CRYOHOLDER
TemperatureAverage: 50 K
DateMar 21, 2009
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 490 / Average electron dose: 20 e/Å2 / Bits/pixel: 16

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.6 °
Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER
Details1-start helix (166.6 degree, 27.6 angstrom) is left handed. F-actin looks like a two strand ribbon. The long pitch helix along the strand of F-actin is right handed.

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