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- EMDB-6977: Enterococcus hirae V-ATPase -

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Basic information

Entry
Database: EMDB / ID: EMD-6977
TitleEnterococcus hirae V-ATPase
Map dataCryo-EM map of EhV-ATPase at 17A
Sample
  • Complex: Enterococcus hirae V-ATPase
Biological speciesEnterococcus hirae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
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 /
Abstract: EhV-ATPase is an ATP-driven Na pump in the eubacteria Enterococcus hirae (Eh). Here, we present the first entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-electron ...EhV-ATPase is an ATP-driven Na pump in the eubacteria Enterococcus hirae (Eh). Here, we present the first entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-electron microscopy (cryo-EM) using Zernike phase plate. The cryo-EM map dominantly showed one of three catalytic conformations in this rotary enzyme. To further stabilize the originally heterogeneous structure caused by the ATP hydrolysis states of the V-ATPases, a peptide epitope tag system was adopted, in which the inserted peptide epitope sequence interfered with rotation of the central rotor by binding the Fab. As a result, the map unexpectedly showed another catalytic conformation of EhV-ATPase. Interestingly, these two conformations identified with and without Fab conversely coincided with those of the minor state 2 and the major state 1 of Thermus thermophilus V/A-ATPase, respectively. The most prominent feature in EhV-ATPase was the off-axis rotor, where the cytoplasmic V domain was connected to the transmembrane V domain through the off-axis central rotor. Furthermore, compared to the structure of ATP synthases, the larger size of the interface between the transmembrane a-subunit and c-ring of EhV-ATPase would be more advantageous for active ion pumping.
History
DepositionJun 1, 2018-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0237
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0237
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6977.png

Downloads & links

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Map

FileDownload / File: emd_6977.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of EhV-ATPase at 17A
Voxel sizeX=Y=Z: 1.99 Å
Density
Contour LevelBy AUTHOR: 0.0237 / Movie #1: 0.0237
Minimum - Maximum-0.023832576 - 0.06566976
Average (Standard dev.)0.001024352 (±0.0074358066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 398.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.991.991.99
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z398.000398.000398.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0240.0660.001

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Supplemental data

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Sample components

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Entire : Enterococcus hirae V-ATPase

EntireName: Enterococcus hirae V-ATPase
Components
  • Complex: Enterococcus hirae V-ATPase

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Supramolecule #1: Enterococcus hirae V-ATPase

SupramoleculeName: Enterococcus hirae V-ATPase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Enterococcus hirae (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Sugar embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 20.0 e/Å2

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64158
FSC plot (resolution estimation)

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