3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-5301

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
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres
List of similar structure data Omokage searchabout Omokage system
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