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Electron cryomicroscopy of the bovine mitochondrial ATP synthase

by single particle reconstruction, at 18.0 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.3, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.3, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2091
AuthorsBaker LA, Watt IN, Runswick MJ, Walker JE, Rubinstein JL
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.3, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.3, Made by UCSF CHIMERA

Supplemental images

image2091.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-2011

EMDB-5335

EMDB-1357

EMDB-1891
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 29, Page 11675-80, Year 2012
TitleArrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM.
AuthorsLindsay A Baker, Ian N Watt, Michael J Runswick, John E Walker, John L Rubinstein
Molecular Structure and Function Program, Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 1X8.
KeywordsAnimals, Cattle, Cryoelectron Microscopy (methods), Mitochondrial Proton-Translocating ATPases (chemistry, 3.6.3.-), Models, Molecular, Protein Conformation, Protein Subunits (chemistry), Protons
LinksDOI: 10.1073/pnas.1204935109, PubMed: 22753497, PMC: PMC3406826
Map
FileEMD-2091.map ( map file in CCP4 format, 8390 KB )
Projections & SlicesSize of images:
AxesZ (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:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum: -0.08318548 - 0.80262011
Average (Standard dev.): 0.01990009 (0.09413327)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : 128 128 128
Limit : 255 255 255
Spacing : 128 128 128
Unit CellA = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.8 A , Y = 2.8 A , Z = 2.8 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS128128128
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0830.8030.020
Annotation Details3D map of bovine ATP synthase
Supplement
Mask Set
Mask: #0
FileEMD-2091.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.11226925 , max. = 0.84195054 , avg. = 0.00089580 , std. = 0.02116470
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #1
FileEMD-2091_1.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.09097404 , max. = 0.79653007 , avg. = 0.00067412 , std. = 0.01770518
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #2
FileEMD-2091_2.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.09690454 , max. = 0.74262875 , avg. = 0.00070010 , std. = 0.01732904
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #3
FileEMD-2091_3.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.10004541 , max. = 0.83061761 , avg. = 0.00067346 , std. = 0.01792759
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #4
FileEMD-2091_4.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.09118840 , max. = 0.85799587 , avg. = 0.00069594 , std. = 0.01852896
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #5
FileEMD-2091_5.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.10822216 , max. = 0.82318503 , avg. = 0.00064184 , std. = 0.01725436
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #6
FileEMD-2091_6.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.09362147 , max. = 0.92726678 , avg. = 0.00059564 , std. = 0.01685107
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #7
FileEMD-2091_7.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.20050630 , max. = 0.79644233 , avg. = 0.00072754 , std. = 0.01818987
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #8
FileEMD-2091_8.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.12422580 , max. = 0.75698125 , avg. = 0.00101709 , std. = 0.01966819
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #9
FileEMD-2091_9.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.21696535 , max. = 0.68578714 , avg. = 0.00195965 , std. = 0.02695820
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Mask: #10
FileEMD-2091_10.msk ( map file in CCP4 format, 8390 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)
Data TypeImage stored as Reals
Dimensions 128 , 128 , 128
Origin 0 , 0 , 0
Limit 127 , 127 , 127
Spacing 128 , 128 , 128
Cell A = 358.4 A , B = 358.4 A , C = 358.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Axis Order X - Y - Z
Statistics min. = -0.16313432 , max. = 0.78987145 , avg. = 0.00068606 , std. = 0.01656608
Space Group Number1
Details::::EMDATABANK.org::::
Pixel Spacing X = 2.8 A , Y = 2.8 A , Z = 2.8 A
Images
Images

image2091.png
Sample
NameBovine mitochondrial ATP synthase
Number of Components1
Oligomeric StateOne hetero oligomeric ATP synthase complex
Theoretical Mass0.6 MDa
DetailsThe sample was maintained in a buffer containing the detergent dodecylmaltoside and phospholipids
Mass-estimation MethodSize exclusion
Experimental Mass0.6 MDa
Component #1: protein - ATPase, complex V
Scientific nameATP synthase
Common NameATPase, complex V
Theoretical Mass0.6 MDa
Experimental Mass0.6 MDa
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesBos taurus (NCBI Taxonomy: 9913)

Common Name of SpeciesCow
Recombinant expressionNo
Natural SourceOrgan Or Tissue: Heart
Organelle: Mitochondria
Cell Location: Mitochondrial membrane
Experiment
Sample Preparation
Specimen Conc2.5 mg/ml
Specimen Support DetailsQuantifoil R2/2 grids
Specimen Stateparticle
BufferDetails: 20 mM Tris-HCl, 100 mM NaCl, 2 mM MgSO4, 1 mM ATP, 0.02%[w/v] sodium azide, 0.1 % dodecylmaltoside, 0.1 mg/ml lipids (cardiolipin:PE:PC 3:1:1)
pH: 7.8
Vitrification
MethodEquilibrate 30 s, blot 10 s
Cryogen NameETHANE
Humidity100
InstrumentFEI VITROBOT MARK III
Imaging
MicroscopeFEI TECNAI F20
Date01-JAN-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose25 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
Astigmatismmanual astigmatism correction using image FFT
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus3000 nm - 7000 nm
Specimen Holder
HolderGatan 626 ( GATAN LIQUID NITROGEN )
Camera
DetectorKodak SO163
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images848
Sampling Size7 microns
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmRotan, Projection matching
SoftwareSpider, Rotan, Frealign, Build_fspace
CTF CorrectionEach particle
Resolution By Author18.0
Resolution MethodFSC at 0.143
Single Particle
Number of Projections57885
Download
Data from EMDB
Header (meta data in XML format)emd-2091.xml (30.8 KB)
Map dataemd_2091.map.gz (7.4 MB)
Imagesimage2091.png (48.2 KB)
Masks (Map data of sub-region, etc)emd_2091_msk.map (8 MB)
emd_2091_msk_1.map (8 MB)
emd_2091_msk_10.map (8 MB)
emd_2091_msk_2.map (8 MB)
emd_2091_msk_3.map (8 MB)
emd_2091_msk_4.map (8 MB)
emd_2091_msk_5.map (8 MB)
emd_2091_msk_6.map (8 MB)
emd_2091_msk_7.map (8 MB)
emd_2091_msk_8.map (8 MB)
emd_2091_msk_9.map (8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2091
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 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), 4.4 MB
Session file for UCSF-Chimera, 26.5 KB