EMDB-1357: Structure of the mitochondrial ATP synthase by electro...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1357
Title	Structure of the mitochondrial ATP synthase by electron cryomicroscopy.
Map	3-D model of detergent solubilized bovine ATP synthase
Sample	Bovine mitochondrial ATP synthase
Authors	Rubinstein JL, Walker JE, Henderson R
Date	Deposition: 2007-05-08, Header release: 2007-05-09, Map release: 2007-05-09, Last update: 2011-05-26
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.167303869, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.167303869, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1qo1, Surface level: 0.167303869, Made by UCSF CHIMERA
Supplemental images	1357.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-2011 PDB-3ixw EMDB-1891 PDB-3ixv EMDB-2091 List of similar structure data about Omokage system

Article
Citation - Primary
Article	EMBO J., Vol. 22, Issue 23, Page 6182-92, Year 2003
Title	Structure of the mitochondrial ATP synthase by electron cryomicroscopy.
Authors	John L Rubinstein, John E Walker, Richard Henderson MRC Laboratory of Molecular Biology, Hills Road,Cambridge CB2 2QH, UK.
Keywords	Animals, Cattle, Cryoelectron Microscopy, Image Processing, Computer-Assisted, Mitochondria, Heart (enzymology), Mitochondrial Proton-Translocating ATPases (chemistry, 3.6.3.-), Models, Molecular, Protein Conformation, Protein Structure, Secondary, Rotation
Links	PubMed: 14633978, DOI: 10.1093/emboj/cdg608, PMC: PMC291849

Map

File

EMD-1357.map ( map file in CCP4 format, 8389 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:	0.0799, 0.1673039 (movie #1):
Minimum - Maximum:	-0.14835 - 0.899798
Average (Standard dev.):	0.01476 (0.0974465)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	128	128	128
Origin :	0	0	0
Limit :	127	127	127
Spacing :	128	128	128

Unit Cell

A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.8 A , Y = 2.8 A , Z = 2.8 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.8	2.8	2.8
M x/y/z	128	128	128
origin x/y/z	0.000	0.000	0.000
length x/y/z	358.400	358.400	358.400
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-64	-64	-64
NX/NY/NZ	128	128	128
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	128	128	128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-0.148	0.900	0.015

Annotation Details

3-D model of detergent solubilized bovine ATP synthase

Supplement
Images
Images	1357.gif

Sample
Name	Bovine mitochondrial ATP synthase
Oligomeric State	multisubunit complex
Number of Components	15
Theoretical Mass	0.66 MDa
Details	Kept in solution with Brij-35 detergent
Component #1: protein - alpha
Scientific name	alpha
Theoretical Mass	0.05439 MDa
Experimental Mass	0.05439 MDa
Details	3 copies
Oligomeric Details	Multiprotein complex
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Natural Source	Organ Or Tissue: Bovine Heart Organelle: Mitochondrial Cell Location: Inner mitochondrial membrane
Component #2: protein - beta
Scientific name	beta
Theoretical Mass	0.051705 MDa
Experimental Mass	0.051705 MDa
Details	3 copies
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #3: protein - gamma
Scientific name	gamma
Theoretical Mass	0.030256 MDa
Experimental Mass	0.030256 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #4: protein - delta
Scientific name	delta
Theoretical Mass	0.015065 MDa
Experimental Mass	0.015065 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #5: protein - epsilon
Scientific name	epsilon
Theoretical Mass	0.005652 MDa
Experimental Mass	0.005652 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #6: protein - a
Scientific name	a
Theoretical Mass	0.024788 MDa
Experimental Mass	0.024788 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #7: protein - b
Scientific name	b
Theoretical Mass	0.024669 MDa
Experimental Mass	0.024669 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #8: protein - c
Scientific name	c
Theoretical Mass	0.007608 MDa
Experimental Mass	0.007608 MDa
Details	9-12 copies
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #9: protein - d
Scientific name	d
Theoretical Mass	0.018561 MDa
Experimental Mass	0.018561 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #10: protein - e
Scientific name	e
Theoretical Mass	0.008321 MDa
Experimental Mass	0.008321 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #11: protein - f
Scientific name	f
Theoretical Mass	0.010166 MDa
Experimental Mass	0.010166 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #12: protein - g
Scientific name	g
Theoretical Mass	0.011286 MDa
Experimental Mass	0.011286 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #13: protein - F6
Scientific name	F6
Theoretical Mass	0.008958 MDa
Experimental Mass	0.008958 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #14: protein - OSCP
Scientific name	OSCP
Theoretical Mass	0.020960 MDa
Experimental Mass	0.020960 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No
Component #15: protein - A6L
Scientific name	A6L
Theoretical Mass	0.007937 MDa
Experimental Mass	0.007937 MDa
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Cow
Recombinant expression	No

Experiment
Sample Preparation
Specimen Conc	3 mg/ml
Specimen Support Details	400 mesh grid coated with a perforated carbon film
Specimen State	particle
Buffer	Details: Tris-HCl, 20 mM Sucrose, 50 mM Magnesium Sulfate, 2 mM EDTA, 1 mM ADP, 2 mM Brij-35, 0.05%(w/v) pH: 8.0
Vitrification
Cryogen Name	ETHANE
Humidity	100
Instrument	HOMEMADE PLUNGER
Method	Sample applied from one side and blotted from same side
Details	Vitrification instrument: Talmon plunger. Carried out in coldroom
Imaging
Microscope	FEI TECNAI F20
Date	2003-01-01
Details	Digitized with Zeiss SCAI scanner
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	10 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X,
Astigmatism	corrected at 175kx magnification
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	3000 nm - 6000 nm
Specimen Holder
Holder	Side entry liquid nitrogen ( GATAN LIQUID NITROGEN )
Camera
Detector	Kodak SO163
Image Acquisition
Number of Digital Images	101
Sampling Size	7 microns
Quant Bit Number	8
Scanner	ZEISS SCAI

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Rotational Analysis
Software	IMAGIC, FREALIGN, ROTAN
CTF Correction	See publication
Resolution By Author	32
Resolution Method	FSC at 0.143 cut-off
Single Particle
Number of Projections	5984
Details	Particles manually selected.
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Software	O
Details	Protocol: Eye. Multiple pdb files fit. See publication.

Download

Data from EMDB

Header (meta data in XML format)

emd-1357.xml (16.4 KB)

Map data

emd_1357.map.gz (7.4 MB)

Images

1357.gif (41.3 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1357

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 19.6 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.5 MB Session file for UCSF-Chimera, 19.8 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 4.7 MB Session file for UCSF-Chimera, 1.2 MB