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

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Basic information

Database: EMDB / ID: 6179
TitleOne state of F-Actin at near-atomic resolution
Keywordshelical polymer / actin filament
SampleSkeletal muscle actin
SourceOryctolagus cuniculus / mammal / rabbit / アナウサギ /
Map datareconstruction of F-actin
Methodhelical reconstruction, at 4.7 Å resolution
AuthorsGalkin VE / Orlova A / Vos MR / Schroder GF / Egelman EH
CitationStructure, 2015, 23, 173-182

Structure, 2015, 23, 173-182 Yorodumi Papers
Near-atomic resolution for one state of F-actin.
Vitold E Galkin / Albina Orlova / Matthijn R Vos / Gunnar F Schröder / Edward H Egelman

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

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • 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
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 168 Å / B: 168 Å / C: 209.99998 Å
α=β=γ: 90 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
start NX/NY/NZ-72-72-72
MAP C/R/S123
start NC/NR/NS-79-79-99
D min/max/mean-0.0890.150-0.009

Supplemental data

Sample components

Entire Skeletal muscle actin

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

Component #1: protein, actin

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

Experimental details

Sample preparation

Specimen statefilament
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 %

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
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 850

Image processing

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

Atomic model buiding

Output model

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