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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: 5301
TitleNegative Stain reconstruction of the Thermus thermophilus A-ATPase to 23 Angstrom. Opposite Hand to published.
KeywordsA-ATPase / Thermus thermophilus / ATPase
SampleThermus thermophilus A-ATPase
SourceThermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
Map dataThis is a negative stain reconstruction of the Thermus thermophilus A-ATPase
Methodsingle particle reconstruction, at 23 A resolution
AuthorsBernal RA / Stock D
CitationStructure, 2004, 12, 1789-1798

Structure, 2004, 12, 1789-1798 StrPapers
Three-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.
Ricardo A Bernal / Daniela Stock

DateDeposition: Jun 7, 2011 / Header (metadata) release: Jun 9, 2011 / Map release: Jun 9, 2011 / Last update: Jun 7, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_5301.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices
Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.3 A/pix
= 422.4 A
128 pix
3.3 A/pix
= 422.4 A
128 pix
3.3 A/pix
= 422.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.3 A
Density
Contour Level:1.6 (by author), 1.6 (movie #1):
Minimum - Maximum-5.80634 - 15.2002
Average (Standard dev.)1.75237e-09 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
CellA=B=C: 422.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / Number of components: 1 / Oligomeric State: multi-subunit complex

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Component #1: cellular-component, ATPase

Cellular-componentName: ATPase / a.k.a: ATPase / Oligomeric Details: multimer / Recombinant expression: No
SourceSpecies: Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
Strain: HB8
Source (natural)Location in cell: membrane

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.02 mg/ml
Buffer solution: 20 mM Tris, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 0.05% n-dodecyl-beta-D-maltoside, 0.02% NaN3
pH: 8
Support film400 mesh 3.05 mm copper grids with a thin layer carbon support
StainingThree 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.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Jan 22, 2003
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal), 42000 X (calibrated) / Astigmatism: not corrected / Imaging mode: BRIGHT FIELD / Defocus: 1000 nm
Specimen HolderHolder: side entry single tilt / Model: OTHER / Temperature: 25 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 60 / Number of projections: 12300 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Cross-common lines / Software: MRC Image2000 and Imagic
CTF correction: no ctf correction done because it was a negative stain reconstruction
Resolution: 23 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: EMfit / Refinement protocol: rigid body / Target criteria: sumf and number of atoms inside density / Refinement space: REAL
Details: 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.
Input PDB model: 1E79
Chain ID: 1E79_A, 1E79_B, 1E79_C, 1E79_D, 1E79_E, 1E79_F, 1E79_G
Modeling #2Software: EMfit / Refinement protocol: rigid body / Target criteria: sumf and number of atoms inside density / Refinement space: REAL
Details: 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.
Input PDB model: 1R5Z
Chain ID: 1R5Z_A, 1R5Z_B, 1R5Z_C
Modeling #3Software: EMfit / Refinement protocol: rigid body / Target criteria: sumf and number of atoms inside density / Refinement space: REAL
Details: 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.
Input PDB model: 1C17
Chain ID: 1C17_A, 1C17_B, 1C17_C, 1C17_D, 1C17_E, 1C17_F, 1C17_G, 1C17_H, 1C17_I, 1C17_J, 1C17_K, 1C17_L

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