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- EMDB-9662: 19A ZPC cryo-EM map of Eh V-ATPase-Fab -

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Basic information

Entry
Database: EMDB / ID: 9662
Title19A ZPC cryo-EM map of Eh V-ATPase-Fab
Map data19A ZPC cryo-EM map of Eh V-ATPase-Fab
SampleEnterococcus hirae V-ATPse:
Methodsingle particle reconstruction / cryo EM / 19 Å resolution
AuthorsTsunoda J / Song C / Imai FL / Murata T / Ueno H / Iino R / Takagi J / Murata K
CitationJournal: Sci Rep / Year: 2018
Title: Off-axis rotor in Enterococcus hirae V-ATPase visualized by Zernike phase plate single-particle cryo-electron microscopy.
Authors: Jun Tsunoda / Chihong Song / Fabiana Lica Imai / Junichi Takagi / Hiroshi Ueno / Takeshi Murata / Ryota Iino / Kazuyoshi Murata
DateDeposition: Sep 23, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0262
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0262
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9662.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.99 Å/pix.
= 398.4 Å
200 pix
1.99 Å/pix.
= 398.4 Å
200 pix
1.99 Å/pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.992 Å
Density
Contour Level:0.0262 (by author), 0.0262 (movie #1):
Minimum - Maximum-0.04633683 - 0.08095652
Average (Standard dev.)0.0013634621 (0.00937568)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 398.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9921.9921.992
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z398.400398.400398.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0460.0810.001

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Supplemental data

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Sample components

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Entire Enterococcus hirae V-ATPse

EntireName: Enterococcus hirae V-ATPse / Number of components: 1

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Component #1: protein, Enterococcus hirae V-ATPse

ProteinName: Enterococcus hirae V-ATPse / Recombinant expression: No
MassExperimental: 800 MDa
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 95 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 30000.0 X (nominal), 32129.0 X (calibrated) / Cs: 4.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 250.0 - 500.0 nm / Energy filter: In-column Omega Filter
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 76.0 - 76.0 K)
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image acquisition

Image acquisitionNumber of digital images: 1302 / Sampling size: 6.4 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 35413
3D reconstructionSoftware: RELION / Resolution: 19 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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