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- EMDB-7036: Cryo-EM structure of the dimeric FO region of yeast mitochondrial... -

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Basic information

Entry
Database: EMDB / ID: 7036
TitleCryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase
SampleYeast mitochondrial ATP synthase FO complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map dataSharpened map of the dimeric FO region of yeast mitochondrial ATP synthase
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsGuo H / Rubinstein JL
CitationScience, 2017

Science, 2017 Yorodumi Papers
Atomic model for the dimeric FO region of mitochondrial ATP synthase.
Hui Guo / Stephanie A Bueler / John L Rubinstein

Validation ReportPDB-ID: 6b2z

SummaryFull reportAbout validation report
DateDeposition: Sep 20, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 15, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.19
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.19
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6b2z
  • Surface level: 0.19
  • Imaged by UCSF CHIMERA
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_7036.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.06 Å/pix.
= 339.2 Å
320 pix
1.06 Å/pix.
= 339.2 Å
320 pix
1.06 Å/pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.165 (by author), 0.19 (movie #1):
Minimum - Maximum-0.7367223 - 1.1907687
Average (Standard dev.)0.0009854478 (0.03345717)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.7371.1910.001

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Supplemental data

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Mask #1

Fileemd_7036_msk_1.map ( map file in CCP4 format, 131073 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsMask used for calculating FSC of the dimeric FO region of yeast mitochondrial ATP synthase
Space group number1

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Mask #1~

Fileemd_7036_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Yeast mitochondrial ATP synthase FO complex

EntireName: Yeast mitochondrial ATP synthase FO complex / Number of components: 11
MassTheoretical: 400 kDa

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Component #1: protein, Yeast mitochondrial ATP synthase FO complex

ProteinName: Yeast mitochondrial ATP synthase FO complex / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Strain: W303-1A
Source (natural)Organelle: Mitochondria / Location in cell: Inner membrane of mitochondria

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Component #2: protein, ATP synthase subunit c, mitochondrial

ProteinName: ATP synthase subunit c, mitochondrial / Recombinant expression: No
MassTheoretical: 7.762375 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #3: protein, ATP synthase protein 8

ProteinName: ATP synthase protein 8 / Recombinant expression: No
MassTheoretical: 5.825215 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #4: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Recombinant expression: No
MassTheoretical: 27.90043 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #5: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Recombinant expression: No
MassTheoretical: 23.194498 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Strain: W303-1A

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Component #6: protein, ATP synthase subunit d, mitochondrial

ProteinName: ATP synthase subunit d, mitochondrial / Recombinant expression: No
MassTheoretical: 19.709424 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #7: protein, ATP synthase subunit e, mitochondrial

ProteinName: ATP synthase subunit e, mitochondrial / Recombinant expression: No
MassTheoretical: 4.188154 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #8: protein, ATP synthase subunit f, mitochondrial

ProteinName: ATP synthase subunit f, mitochondrial / Recombinant expression: No
MassTheoretical: 10.584166 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #9: protein, ATP synthase subunit g

ProteinName: ATP synthase subunit g / Recombinant expression: No
MassTheoretical: 9.039134 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Strain: W303-1A

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Component #10: protein, ATP synthase subunit j, mitochondrial

ProteinName: ATP synthase subunit j, mitochondrial / Recombinant expression: No
MassTheoretical: 6.696771 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #11: protein, ATP synthase subunit k, mitochondrial

ProteinName: ATP synthase subunit k, mitochondrial / Recombinant expression: No
MassTheoretical: 7.546778 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Temperature: 277 K / Humidity: 100 % / Details: blot for 26 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 71 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000 X (nominal), 47170 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3023

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 238848
3D reconstructionSoftware: cryoSPARC / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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