EMDB-5301: Negative Stain reconstruction of the Thermus thermophi...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5301
Title	Negative Stain reconstruction of the Thermus thermophilus A-ATPase to 23 Angstrom. Opposite Hand to published.
Map	This is a negative stain reconstruction of the Thermus thermophilus A-ATPase
Sample	Thermus thermophilus A-ATPase
Keywords	A-ATPase, Thermus thermophilus, ATPase
Authors	Bernal RA, Stock D
Date	Deposition: 2011-06-07, Header release: 2011-06-09, Map release: 2011-06-09, Last update: 2011-09-12
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 1.6, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.6, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-5335 EMDB-1542 EMDB-1888 EMDB-2011 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Structure, Vol. 12, Issue 10, Page 1789-98, Year 2004
Title	Three-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.
Authors	Ricardo A Bernal, Daniela Stock MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.
Keywords	Animals, 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.-)
Links	PubMed: 15458628, DOI: 10.1016/j.str.2004.07.017, PII: S0969212604002862

Map

File

EMD-5301.map ( map file in CCP4 format, 8390 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	1.6 (by author), 1.6 (movie #1):
Minimum - Maximum:	-5.80634 - 15.2002
Average (Standard dev.):	1.75237e-09 (1)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	128	128	128
Origin :	-64	-64	-64
Limit :	63	63	63
Spacing :	128	128	128

Unit Cell

A = 422.4 A , B = 422.4 A , C = 422.4 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 3.3 A , Y = 3.3 A , Z = 3.3 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	3.3	3.3	3.3
M x/y/z	128	128	128
origin x/y/z	0.000	0.000	0.000
length x/y/z	422.400	422.400	422.400
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-62	-62	-62
NX/NY/NZ	125	125	125
MAP C/R/S	1	2	3
start NC/NR/NS	-64	-64	-64
NC/NR/NS	128	128	128
start NC,NX/NR,NY/NS,NZ	-64	-64	-64
NC,NX/NR,NY/NS,NZ	128	128	128
D min/max/mean	-5.806	15.200	0.000

Annotation Details

This is a negative stain reconstruction of the Thermus thermophilus A-ATPase

Supplement

Sample
Name	Thermus thermophilus A-ATPase
Number of Components	1
Oligomeric State	multi-subunit complex
Component #1: cellular-component - ATPase
Scientific name	ATPase
Oligomeric Details	multimer
Scientific Name of Species	Thermus thermophilus (NCBI Taxonomy: 274)
Common Name of Species	Thermus thermophilus
Strain	HB8
Recombinant expression	No
Natural Source	Cell Location: membrane

Experiment
Sample Preparation
Staining	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.
Specimen Conc	0.02 mg/ml
Specimen Support Details	400 mesh 3.05 mm copper grids with a thin layer carbon support
Specimen State	particle
Buffer	Details: 20 mM Tris, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 0.05% n-dodecyl-beta-D-maltoside, 0.02% NaN3 pH: 8.0
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI 12
Date	22-JAN-2003
Electron Gun
Electron Source	LAB6
Accelerating Voltage	120 kV
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 42000 X, Calibrated: 42000 X
Astigmatism	not corrected
Imaging Mode	BRIGHT FIELD
Defocus	1000 nm - 1000 nm
Specimen Holder
Holder	side entry single tilt ( OTHER )
Temperature	25 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	ZEISS SCAI
Sampling Size	14 microns
Quant Bit Number	8

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Cross-common lines
Software	MRC Image2000 and Imagic
CTF Correction	no ctf correction done because it was a negative stain reconstruction
Resolution By Author	23
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Class Averages	60
Number of Projections	12300
Atomic Model Fitting
Model #0
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.
Refinement Protocol	rigid body
Refinement Space	REAL
Target Criteria	sumf and number of atoms inside density
Software	EMfit
Model #1
Refinement Space	REAL
Target Criteria	sumf and number of atoms inside density
Refinement Protocol	rigid body
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.
Software	EMfit
Model #2
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.
Software	EMfit
Refinement Protocol	rigid body
Target Criteria	sumf and number of atoms inside density
Refinement Space	REAL

Download

Data from EMDB

Header (meta data in XML format)

emd-5301.xml (10.2 KB)

Map data

emd_5301.map.gz (7.5 MB)

FTP directory

ftp://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