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- EMDB-2781: Structure of the vacuolar H+-ATPase rotary motor at subnanometer ... -

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Basic information

Entry
Database: EMDB / ID: EMD-2781
TitleStructure of the vacuolar H+-ATPase rotary motor at subnanometer resolution
Map dataV-ATPase reconstruction
Sample
  • Sample: Manduca sexta vacuolar ATPase complex
  • Organelle or cellular component: Vacuolar ATPase
KeywordsRotary ATPase / vacuolar ATPase
Biological speciesManduca sexta (tobacco hornworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsRawson S / Phillips C / Huss M / Tiburcy F / Wieczorek H / Trinick J / Harrison MA / Muench SP
CitationJournal: Structure / Year: 2015
Title: Structure of the vacuolar H+-ATPase rotary motor reveals new mechanistic insights.
Authors: Shaun Rawson / Clair Phillips / Markus Huss / Felix Tiburcy / Helmut Wieczorek / John Trinick / Michael A Harrison / Stephen P Muench /
Abstract: Vacuolar H(+)-ATPases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. Here we report a ∼ 1 nm resolution ...Vacuolar H(+)-ATPases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. Here we report a ∼ 1 nm resolution reconstruction of a V-ATPase in a different conformational state from that previously reported for a lower-resolution yeast model. The stator network of the V-ATPase (and by implication that of other rotary ATPases) does not change conformation in different catalytic states, and hence must be relatively rigid. We also demonstrate that a conserved bearing in the catalytic domain is electrostatic, contributing to the extraordinarily high efficiency of rotary ATPases. Analysis of the rotor axle/membrane pump interface suggests how rotary ATPases accommodate different c ring stoichiometries while maintaining high efficiency. The model provides evidence for a half channel in the proton pump, supporting theoretical models of ion translocation. Our refined model therefore provides new insights into the structure and mechanics of the V-ATPases.
History
DepositionSep 5, 2014-
Header (metadata) releaseSep 24, 2014-
Map releaseFeb 18, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emdbpicture....

Downloads & links

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Map

FileDownload / File: emd_2781.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV-ATPase reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-2.55582762 - 13.69235134
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.55613.6920.000

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Supplemental data

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Sample components

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Entire : Manduca sexta vacuolar ATPase complex

EntireName: Manduca sexta vacuolar ATPase complex
Components
  • Sample: Manduca sexta vacuolar ATPase complex
  • Organelle or cellular component: Vacuolar ATPase

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Supramolecule #1000: Manduca sexta vacuolar ATPase complex

SupramoleculeName: Manduca sexta vacuolar ATPase complex / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: monomeric / Number unique components: 1
Molecular weightExperimental: 900 KDa / Method: mass spec

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Supramolecule #1: Vacuolar ATPase

SupramoleculeName: Vacuolar ATPase / type: organelle_or_cellular_component / ID: 1 / Name.synonym: V-ATPase / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Manduca sexta (tobacco hornworm) / synonym: tobacco hornworm
Molecular weightExperimental: 900 KDa

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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

Concentration0.025 mg/mL
BufferpH: 8.1
Details: 150 mM NaCl, 20 mM Tris-HCl, 9.6 mM 2-mercaptoethanol, 0.01% C12E10
GridDetails: 400 mesh Quantifoil R2.0/2.0 grids with thin carbon (10 nm) coating, glow discharged in air.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: Grids were blotted for 7.5 seconds

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsCollected with FEI EPU software
DateFeb 27, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1366 / Average electron dose: 60 e/Å2
Details: Each micrograph is sum of 34 frames recorded by direct detector.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 103704 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsStandard procedures in RELION1.3
CTF correctionDetails: Relion
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: OTHER / Software - Name: Relion
Details: Maximum likelihood in Relion using 3D auto-refine. The particles were handpicked in BOXER
Number images used: 6714

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