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- EMDB-7937: Cryo-EM structure of ADP-Pi-actin filaments -

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Basic information

Entry
Database: EMDB / ID: 7937
TitleCryo-EM structure of ADP-Pi-actin filaments
Map dataADP-Pi-actin
SampleADP-Pi-actin:
Actin, alpha skeletal muscle / (ligand) x 3
Function / homologyActin family / Actin, conserved site / Actin/actin-like conserved site / Actin / Actins signature 1. / Actins signature 2. / Actins and actin-related proteins signature. / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development ...Actin family / Actin, conserved site / Actin/actin-like conserved site / Actin / Actins signature 1. / Actins signature 2. / Actins and actin-related proteins signature. / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / ATP binding / Actin, alpha skeletal muscle
Function and homology information
SourceGallus gallus (chicken) / Chicken (chicken)
Methodhelical reconstruction / cryo EM / 3.1 Å resolution
AuthorsChou SZ / Pollard TD
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides.
Authors: Steven Z Chou / Thomas D Pollard
Validation ReportPDB-ID: 6djn

SummaryFull reportAbout validation report
DateDeposition: May 25, 2018 / Header (metadata) release: Jun 20, 2018 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6djn
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7937.map.gz (map file in CCP4 format, 141151 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
328 pix
1.05 Å/pix.
= 342.76 Å
328 pix
1.05 Å/pix.
= 342.76 Å
328 pix
1.05 Å/pix.
= 342.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density
Contour Level:0.018 (by author), 0.018 (movie #1):
Minimum - Maximum-0.044236768 - 0.12977494
Average (Standard dev.)0.000120939 (0.0022501482)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions328328328
Origin0.00.00.0
Limit327.0327.0327.0
Spacing328328328
CellA=B=C: 342.75998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z328328328
origin x/y/z0.0000.0000.000
length x/y/z342.760342.760342.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS328328328
D min/max/mean-0.0440.1300.000

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Supplemental data

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Sample components

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Entire ADP-Pi-actin

EntireName: ADP-Pi-actin / Number of components: 5

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Component #1: protein, ADP-Pi-actin

ProteinName: ADP-Pi-actin / Recombinant expression: No
SourceSpecies: Gallus gallus (chicken)

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Component #2: protein, Actin, alpha skeletal muscle

ProteinName: Actin, alpha skeletal muscle / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 41.875633 kDa
SourceSpecies: Chicken (chicken)

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Component #3: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #5: ligand, PHOSPHATE ION

LigandName: PHOSPHATE IONPhosphate / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 9.497105 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 27.42 Å / Delta phi: -166.56 deg.
Sample solutionpH: 7
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 43.54 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient
Output model

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