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Negative Stain reconstruction of the Thermus thermophilus A-ATPase to 23 Angstrom. Opposite Hand to published.

by single particle reconstruction, at 23 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.6, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.6, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5301
TitleNegative Stain reconstruction of the Thermus thermophilus A-ATPase to 23 Angstrom. Opposite Hand to published.
MapThis is a negative stain reconstruction of the Thermus thermophilus A-ATPase
SampleThermus thermophilus A-ATPase
KeywordsA-ATPase, Thermus thermophilus, ATPase
AuthorsBernal RA, Stock D
DateDeposition: 2011-06-07, Header release: 2011-06-09, Map release: 2011-06-09, Last update: 2011-09-12
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.6, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.6, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleStructure, Vol. 12, Issue 10, Page 1789-98, Year 2004
TitleThree-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.
AuthorsRicardo A Bernal, Daniela Stock
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.
KeywordsAnimals, Cattle, Crystallography, X-Ray, Microscopy, Electron, Models, Molecular, Protein Structure, Quaternary, Structural Homology, Protein, Thermus thermophilus (enzymology), Vacuolar Proton-Translocating ATPases (chemistry, 3.6.1.-)
LinksPubMed: 15458628, DOI: 10.1016/j.str.2004.07.017, PII: S0969212604002862
Map
Fileemd_5301.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:1.6 (by author), 1.6 (movie #1):
Minimum - Maximum: -5.80634 - 15.2002
Average (Standard dev.): 1.75237e-09 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
Unit CellA= B= C: 422.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.3 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.80615.2000.000
Annotation DetailsThis is a negative stain reconstruction of the Thermus thermophilus A-ATPase
Supplement
Images
Images
Sample
NameThermus thermophilus A-ATPase
Number of Components1
Oligomeric Statemulti-subunit complex
Component #1: cellular-component - ATPase
Scientific nameATPase
Oligomeric Detailsmultimer
Scientific Name of SpeciesThermus thermophilus
Common Name of SpeciesThermus thermophilus
NCBI taxonomy274
StrainHB8
Recombinant expressionNo
Natural SourceCell Location: membrane
Experiment
Sample Preparation
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.
Specimen Conc0.02 mg/ml
Specimen Support Details400 mesh 3.05 mm copper grids with a thin layer carbon support
Specimen Stateparticle
BufferDetails: 20 mM Tris, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 0.05% n-dodecyl-beta-D-maltoside, 0.02% NaN3
pH: 8
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date22-JAN-2003
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 42000, Calibrated: 42000
Astigmatismnot corrected
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 1000 nm
Specimen Holder
Holderside entry single tilt
ModelOTHER
Temperature25 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerZEISS SCAI
Sampling Size14
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCross-common lines
SoftwareMRC Image2000 and Imagic
CTF Correctionno ctf correction done because it was a negative stain reconstruction
Resolution By Author23 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages60
Number of Projections12300
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
DetailsProtocol: 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.
Refinement Protocolrigid body
Refinement SpaceREAL
Target Criteriasumf and number of atoms inside density
SoftwareEMfit
PDB Entry ID1E79
PDB Chain ID1E79_A, 1E79_B, 1E79_C, 1E79_D, 1E79_E, 1E79_F, 1E79_G
Model #1
Refinement SpaceREAL
Target Criteriasumf and number of atoms inside density
Refinement Protocolrigid body
DetailsProtocol: 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.
SoftwareEMfit
PDB Entry ID1R5Z
PDB Chain ID1R5Z_A, 1R5Z_B, 1R5Z_C
Model #2
DetailsProtocol: 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.
SoftwareEMfit
Refinement Protocolrigid body
Target Criteriasumf and number of atoms inside density
Refinement SpaceREAL
PDB Entry ID1C17
PDB Chain ID1C17_A, 1C17_B, 1C17_C, 1C17_D, 1C17_E, 1C17_F, 1C17_G, 1C17_H, 1C17_I, 1C17_J, 1C17_K, 1C17_L
Download
Data from EMDB
Header (meta data in XML format)emd-5301.xml (10.3 KB)
Map dataemd_5301.map.gz (7.5 MB)
Imagesemd_5301_1.jpg (118.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5301
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.7 KB