[English] 日本語
Yorodumi
- EMDB-2781: Structure of the vacuolar H+-ATPase rotary motor at subnanometer ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 2781
TitleStructure of the vacuolar H+-ATPase rotary motor at subnanometer resolution
Map dataV-ATPase reconstruction
SampleManduca sexta vacuolar ATPase complex:
Vacuolar ATPaseV-ATPase
KeywordsRotary ATPase / vacuolar ATPase
SourceManduca sexta (tobacco hornworm)
Methodsingle particle reconstruction / cryo EM / 9.4 Å resolution
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.
DateDeposition: Sep 5, 2014 / Header (metadata) release: Sep 24, 2014 / Map release: Feb 18, 2015 / Last update: Feb 17, 2016

-
Structure visualization

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

Downloads & links

-
Map

Fileemd_2781.map.gz (map file in CCP4 format, 128001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.35 Å/pix.
= 432. Å
320 pix
1.35 Å/pix.
= 432. Å
320 pix
1.35 Å/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
Contour Level:4.00 (by author), 4 (movie #1):
Minimum - Maximum-2.55582762 - 13.69235134
Average (Standard dev.)0E-8 (1.00000000)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 432.0 Å
α=β=γ: 90.0 deg.

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

-
Supplemental data

-
Sample components

-
Entire Manduca sexta vacuolar ATPase complex

EntireName: Manduca sexta vacuolar ATPase complex / Details: monodisperse / Number of components: 1 / Oligomeric State: monomeric
MassExperimental: 900 kDa / Measured by: mass spec

-
Component #1: cellular-component, Vacuolar ATPase

Cellular-componentName: Vacuolar ATPaseV-ATPase / a.k.a: V-ATPase / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 1
MassExperimental: 900 kDa
SourceSpecies: Manduca sexta (tobacco hornworm)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.025 mg/ml
Buffer solution: 150 mM NaCl, 20 mM Tris-HCl, 9.6 mM 2-mercaptoethanol, 0.01% C12E10
pH: 8.1
Support film400 mesh Quantifoil R2.0/2.0 grids with thin carbon (10 nm) coating, glow discharged in air.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 % / Method: Grids were blotted for 7.5 seconds

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Feb 27, 2014 / Details: Collected with FEI EPU software
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 103704 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 5500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1366
Details: Each micrograph is sum of 34 frames recorded by direct detector.

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 6714 / Details: Standard procedures in RELION1.3
3D reconstructionAlgorithm: Maximum Likelihood / Software: Relion / CTF correction: Relion
Details: Maximum likelihood in Relion using 3D auto-refine. The particles were handpicked in BOXER
Resolution: 9.4 Å / Resolution method: FSC 0.143, gold-standard

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more