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- EMDB-5301: Negative Stain reconstruction of the Thermus thermophilus A-ATPas... -

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Basic information

Entry
Database: EMDB / ID: EMD-5301
TitleNegative Stain reconstruction of the Thermus thermophilus A-ATPase to 23 Angstrom. Opposite Hand to published.
Map dataThis is a negative stain reconstruction of the Thermus thermophilus A-ATPase
Sample
  • Sample: Thermus thermophilus A-ATPase
  • Organelle or cellular component: ATPase
KeywordsA-ATPase / Thermus thermophilus / ATPase
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsBernal RA / Stock D
CitationJournal: Structure / Year: 2004
Title: Three-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.
Authors: Ricardo A Bernal / Daniela Stock /
Abstract: ATPases are unique rotary motors that are essential to all living organisms because of their role in energy interconversion. A three-dimensional reconstruction of the intact H+-ATPase/synthase from ...ATPases are unique rotary motors that are essential to all living organisms because of their role in energy interconversion. A three-dimensional reconstruction of the intact H+-ATPase/synthase from Thermus thermophilus has revealed the presence of two interconnected peripheral stalks, a well-defined central stalk, and a hexagonally shaped hydrophobic domain. The peripheral stalks are each attached to the water soluble sector at a noncatalytic subunit interface and extend down toward the membrane where they interact with a strong elongated tube of density that runs parallel to the membrane and connects the two stalks. The central stalk is well resolved, especially with respect to its interaction with a single catalytic subunit giving rise to an asymmetry comparable to that identified in F-ATPases. The hexagonal shape of the membrane domain might suggest the presence of 12 proteolipids arranged as dimers, analogous to the proposed arrangement in the related eukaryotic V-ATPases.
History
DepositionJun 7, 2011-
Header (metadata) releaseJun 9, 2011-
Map releaseJun 9, 2011-
UpdateSep 12, 2011-
Current statusSep 12, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5301_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5301.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a negative stain reconstruction of the Thermus thermophilus A-ATPase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 128 pix.
= 422.4 Å		3.3 Å/pix.
x 128 pix.
= 422.4 Å		3.3 Å/pix.
x 128 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-5.80634 - 15.200200000000001
Average (Standard dev.)0.00000000175237 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 422.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-5.80615.2000.000

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Supplemental data

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Sample components

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Entire : Thermus thermophilus A-ATPase

EntireName: Thermus thermophilus A-ATPase
Components
  • Sample: Thermus thermophilus A-ATPase
  • Organelle or cellular component: ATPase

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Supramolecule #1000: Thermus thermophilus A-ATPase

SupramoleculeName: Thermus thermophilus A-ATPase / type: sample / ID: 1000 / Oligomeric state: multi-subunit complex / Number unique components: 1

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Supramolecule #1: ATPase

SupramoleculeName: ATPase / type: organelle_or_cellular_component / ID: 1 / Name.synonym: ATPase / Oligomeric state: multimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: HB8 / synonym: Thermus thermophilus / Location in cell: membrane

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
Details: 20 mM Tris, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 0.05% n-dodecyl-beta-D-maltoside, 0.02% NaN3
StainingType: NEGATIVE
Details: Three microliters of the T. thermophilus sample, diluted to 0.02 mg/mL, was placed onto the surface of the carbon-coated grid. The sample was blotted off and replaced with 3 microliters of ...Details: Three microliters of the T. thermophilus sample, diluted to 0.02 mg/mL, was placed onto the surface of the carbon-coated grid. The sample was blotted off and replaced with 3 microliters of 2% uranyl acetate. The uranyl acetate was blotted away and replaced with 3 microliters of 4% methylamine tungstate. The final drop of methylamine tungstate was blotted away and the grid was left to air dry.
GridDetails: 400 mesh 3.05 mm copper grids with a thin layer carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureAverage: 25 K
Alignment procedureLegacy - Astigmatism: not corrected
DateJan 22, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder: side entry single tilt / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: no ctf correction done because it was a negative stain reconstruction
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC Image2000 and Imagic / Number images used: 12300
Final two d classificationNumber classes: 60

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Atomic model buiding 1

Initial modelPDB ID:

1e79


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G
SoftwareName: EMfit
DetailsPDBEntryID_givenInChain. Protocol: Each chain was fit as a separate rigid body. X-ray coordinates for the bovine alpha3 beta3 and gamma sub-assemblies were manually fitted into the EM density using the program O. The program EMfit (Rossmann et al., 2001) was then used in order to obtain a more quantitative fit.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf and number of atoms inside density

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Atomic model buiding 2

Initial modelPDB ID:

1r5z


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: EMfit
DetailsPDBEntryID_givenInChain. Protocol: Each chain was fit as a separate rigid body. X-ray coordinates for the bovine alpha3 beta3 and gamma sub-assemblies were manually fitted into the EM density using the program O. The program EMfit (Rossmann et al., 2001) was then used in order to obtain a more quantitative fit.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf and number of atoms inside density

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Atomic model buiding 3

Initial modelPDB ID:

1c17


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L
SoftwareName: EMfit
DetailsPDBEntryID_givenInChain. Protocol: Each chain was fit as a separate rigid body. X-ray coordinates for the bovine alpha3 beta3 and gamma sub-assemblies were manually fitted into the EM density using the program O. The program EMfit (Rossmann et al., 2001) was then used in order to obtain a more quantitative fit.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf and number of atoms inside density

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