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- EMDB-6179: One state of F-Actin at near-atomic resolution -

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Basic information

Entry
Database: EMDB / ID: 6179
TitleOne state of F-Actin at near-atomic resolution
Map datareconstruction of F-actin
SampleSkeletal muscle actin:
actin
Keywordshelical polymer / actin filament
Function / homologyActin/actin-like conserved site / Actin / Actin, conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding ...Actin/actin-like conserved site / Actin / Actin, conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / actin monomer binding / actin filament bundle assembly / skeletal muscle myofibril / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / calcium-dependent protein binding / cell body / lamellipodium / protein domain specific binding / positive regulation of gene expression / calcium ion binding / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / Actin, alpha skeletal muscle
Function and homology information
SourceOryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / 4.7 Å resolution
AuthorsGalkin VE / Orlova A / Vos MR / Schroder GF / Egelman EH
CitationJournal: Structure / Year: 2015
Title: Near-atomic resolution for one state of F-actin.
Authors: Vitold E Galkin / Albina Orlova / Matthijn R Vos / Gunnar F Schröder / Edward H Egelman
Abstract: Actin functions as a helical polymer, F-actin, but attempts to build an atomic model for this filament have been hampered by the fact that the filament cannot be crystallized and by structural ...Actin functions as a helical polymer, F-actin, but attempts to build an atomic model for this filament have been hampered by the fact that the filament cannot be crystallized and by structural heterogeneity. We have used a direct electron detector, cryo-electron microscopy, and the forces imposed on actin filaments in thin films to reconstruct one state of the filament at 4.7 Å resolution, which allows for building a reliable pseudo-atomic model of F-actin. We also report a different state of the filament where actin protomers adopt a conformation observed in the crystal structure of the G-actin-profilin complex with an open ATP-binding cleft. Comparison of the two structural states provides insights into ATP-hydrolysis and filament dynamics. The atomic model provides a framework for understanding why every buried residue in actin has been under intense selective pressure.
Validation ReportPDB-ID: 3j8i

SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2014 / Header (metadata) release: Dec 24, 2014 / Map release: Jan 14, 2015 / Last update: Jan 14, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3j8i
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

Fileemd_6179.map.gz (map file in CCP4 format, 20001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.05 Å/pix.
= 210. Å
160 pix
1.05 Å/pix.
= 168. Å
160 pix
1.05 Å/pix.
= 168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.08946684 - 0.15020971
Average (Standard dev.)-0.00916722 (0.01587875)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160200
Origin-79-79-99
Limit8080100
Spacing160160200
CellA: 168.0 Å / B: 168.0 Å / C: 209.99998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z160160200
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000210.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS-79-79-99
NC/NR/NS160160200
D min/max/mean-0.0890.150-0.009

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Supplemental data

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Sample components

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Entire Skeletal muscle actin

EntireName: Skeletal muscle actin / Number of components: 1 / Oligomeric State: polymer

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Component #1: protein, actin

ProteinName: actin / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (natural)Organ or tissue: skeletal muscle

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: LEFT HANDED / Delta z: 27.6 Å / Delta phi: 166.7 deg.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Oct 9, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 850

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Image processing

ProcessingMethod: helical reconstruction / Details: IHRSR
3D reconstructionSoftware: EMAN2, Spider / Resolution: 4.7 Å / Resolution method: OTHER

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Atomic model buiding

Output model

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