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- EMDB-1888: Thermus thermophilus V-type (A-type) ATPase at 16 Angstroms resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-1888
TitleThermus thermophilus V-type (A-type) ATPase at 16 Angstroms resolution
Map dataThermus thermophilus V-type (A-type) ATPase
Sample
  • Sample: V/A-ATPase from Thermus thermophilus solubilized with the detergent dodecyl maltoside.
  • Organelle or cellular component: V-ATPase
KeywordsVacuolar type ATPase / V-ATPase / A-ATPase / Thermus thermophilus / ATP synthase / membrane protein
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsLau WCY / Rubinstein JL
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound V(O) motor.
Authors: Wilson C Y Lau / John L Rubinstein /
Abstract: The eubacterium Thermus thermophilus uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over ...The eubacterium Thermus thermophilus uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over eukaryotic V-ATPases for structural analysis and investigation of the mechanism of the enzyme. Here we report the structure of the complex at approximately 16 A resolution as determined by single particle electron cryomicroscopy (cryo-EM). The resolution of the map and our use of cryo-EM, rather than negative stain EM, reveals detailed information about the internal organization of the assembly. We could separate the map into segments corresponding to subunits A and B, the threefold pseudosymmetric C-subunit, a central rotor consisting of subunits D and F, the L-ring, the stator subcomplex consisting of subunits I, E, and G, and a micelle of bound detergent. The architecture of the V(O) region shows a remarkably small area of contact between the I-subunit and the ring of L-subunits and is consistent with a two half-channel model for proton translocation. The arrangement of structural elements in V(O) gives insight into the mechanism of torque generation from proton translocation.
History
DepositionMar 30, 2011-
Header (metadata) releaseApr 8, 2011-
Map releaseApr 8, 2011-
UpdateNov 26, 2014-
Current statusNov 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.425
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.425
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1888.jpg

Downloads & links

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Map

FileDownload / File: emd_1888.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThermus thermophilus V-type (A-type) ATPase
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour LevelBy AUTHOR: 0.425 / Movie #1: 0.425
Minimum - Maximum-0.24713653 - 1.14009678
Average (Standard dev.)0.00813209 (±0.14459489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin363636
Dimensions128128128
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS363636
NC/NR/NS128128128
D min/max/mean-0.2471.1400.008

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Supplemental data

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Supplemental map: EMD1888-A1.map

FileEMD1888-A1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-A2.map

FileEMD1888-A2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-A3.map

FileEMD1888-A3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-B1.map

FileEMD1888-B1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-B2.map

FileEMD1888-B2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-B3.map

FileEMD1888-B3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-C.map

FileEMD1888-C.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Supplemental map: EMD1888-DF.map

FileEMD1888-DF.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Supplemental map: EMD1888-DetMicelle.map

FileEMD1888-DetMicelle.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-IE2G2.map

FileEMD1888-IE2G2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: EMD1888-LRing.map

FileEMD1888-LRing.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Others

Details[Supplementary_Map_Information.txt]
Author has deposited these 11 additional maps that represent segments of
subunits and subcomplexes from the overall map (emd_1888.map)
1.EMD1888-A1.map, Subunit A from pair 1, 2.8 A/pixel, Contour = 0.427
2.EMD1888-A2.map, Subunit A from pair 2, 2.8 A/pixel, Contour = 0.454
3.EMD1888-A3.map, Subunit A from pair 3, 2.8 A/pixel, Contour = 0.406
4.EMD1888-B1.map, Subunit B from pair 1, 2.8 A/pixel, Contour = 0.434
5.EMD1888-B2.map, Subunit B from pair 2, 2.8 A/pixel, Contour = 0.394
6.EMD1888-B3.map, Subunit B from pair 3, 2.8 A/pixel, Contour = 0.363
7.EMD1888-C.map, Subunit C, 2.8 A/pixel, Contour = 0.379
8.EMD1888-DetMicelle.map, Detergent micelle, 2.8 A/pixel, Contour = 0.113
9.EMD1888-DF.map, Subunits D and F, 2.8 A/pixel, Contour = 0.389
10.EMD1888-IE2G2.map, Subunits I, E (x2) and G (x2), 2.8 A/pixel, Contour = 0.363
11.EMD1888-LRing.map, 12mer of subunit L, 2.8 A/pixel, Contour = 0.323

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Sample components

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Entire : V/A-ATPase from Thermus thermophilus solubilized with the deterge...

EntireName: V/A-ATPase from Thermus thermophilus solubilized with the detergent dodecyl maltoside.
Components
  • Sample: V/A-ATPase from Thermus thermophilus solubilized with the detergent dodecyl maltoside.
  • Organelle or cellular component: V-ATPase

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Supramolecule #1000: V/A-ATPase from Thermus thermophilus solubilized with the deterge...

SupramoleculeName: V/A-ATPase from Thermus thermophilus solubilized with the detergent dodecyl maltoside.
type: sample / ID: 1000 / Oligomeric state: Hetero 26mer / Number unique components: 9
Molecular weightTheoretical: 600 KDa

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Supramolecule #1: V-ATPase

SupramoleculeName: V-ATPase / type: organelle_or_cellular_component / ID: 1 / Name.synonym: ATPase / Recombinant expression: No
Source (natural)Organism: Thermus thermophilus (bacteria) / Location in cell: Plasma membrane

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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

Concentration2.0 mg/mL
BufferpH: 8 / Details: 50mM Tris-HCl 150mM NaCL 5mM MgCl2 O.02% DDM
GridDetails: Quantifoil 2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot Mark III / Method: Blot approx. 20 seconds.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Average electron dose: 25 e/Å2 / Details: Images averaged 2x2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: MRC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: Rotan, Frealign / Number images used: 19825
DetailsParticle images were manually selected with Ximdisp.

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