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- PDB-6b2z: Cryo-EM structure of the dimeric FO region of yeast mitochondrial... -

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Entry
Database: PDB / ID: 6b2z
TitleCryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase
Components
  • (ATP synthase subunit ...) x 9
  • ATP synthase protein 8
KeywordsMEMBRANE PROTEIN / Complex / Dimer / Mitochondrial inner membrane / Proton translocation
Function / homologyATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase subunit K / F/V-ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase, F0 complex, subunit B / ATP synthase protein 8, fungi / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit J ...ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase subunit K / F/V-ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase, F0 complex, subunit B / ATP synthase protein 8, fungi / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit J / V-ATPase proteolipid subunit C-like domain / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase subunit C / ATP synthase j chain / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase D chain, mitochondrial (ATP5H) / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / Protein of unknown function (DUF2611) / ATP synthase a subunit signature. / ATP synthase c subunit signature. / ATP synthase, F0 complex, subunit A, active site / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, stator stalk / ATP hydrolysis coupled cation transmembrane transport / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton transmembrane transporter activity / ATP hydrolysis coupled proton transport / ATP synthesis coupled proton transport / mitochondrial intermembrane space / mitochondrial inner membrane / protein complex oligomerization / lipid binding / integral component of membrane / identical protein binding / cytosol / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit K, mitochondrial / ATP synthase subunit f, mitochondrial
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsGuo, H. / Rubinstein, J.L.
CitationJournal: Science / Year: 2017
Title: Atomic model for the dimeric F region of mitochondrial ATP synthase.
Authors: Hui Guo / Stephanie A Bueler / John L Rubinstein
Abstract: Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic ...Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F region turns the rotor that drives ATP synthesis in the soluble F region. Although crystal structures of the F region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F region. Using cryo-electron microscopy, we determined the structure of the dimeric F complex from at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 20, 2017 / Release: Nov 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2017Structure modelrepositoryInitial release
1.1Nov 15, 2017Structure modelDatabase referencescitation_citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
1.2Nov 29, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
1: ATP synthase subunit c, mitochondrial
2: ATP synthase subunit c, mitochondrial
3: ATP synthase subunit c, mitochondrial
4: ATP synthase subunit c, mitochondrial
5: ATP synthase subunit c, mitochondrial
6: ATP synthase subunit c, mitochondrial
7: ATP synthase subunit c, mitochondrial
8: ATP synthase subunit c, mitochondrial
9: ATP synthase subunit c, mitochondrial
0: ATP synthase subunit c, mitochondrial
A: ATP synthase protein 8
a: ATP synthase subunit a
b: ATP synthase subunit b
d: ATP synthase subunit d, mitochondrial
e: ATP synthase subunit e, mitochondrial
f: ATP synthase subunit f, mitochondrial
g: ATP synthase subunit g
i: ATP synthase subunit j, mitochondrial
k: ATP synthase subunit k, mitochondrial
C: ATP synthase subunit c, mitochondrial
D: ATP synthase subunit c, mitochondrial
E: ATP synthase subunit c, mitochondrial
F: ATP synthase subunit c, mitochondrial
G: ATP synthase subunit c, mitochondrial
H: ATP synthase subunit c, mitochondrial
I: ATP synthase subunit c, mitochondrial
J: ATP synthase subunit c, mitochondrial
K: ATP synthase subunit c, mitochondrial
B: ATP synthase subunit c, mitochondrial
L: ATP synthase protein 8
M: ATP synthase subunit a
N: ATP synthase subunit b
O: ATP synthase subunit d, mitochondrial
P: ATP synthase subunit e, mitochondrial
Q: ATP synthase subunit f, mitochondrial
R: ATP synthase subunit g
S: ATP synthase subunit j, mitochondrial
T: ATP synthase subunit k, mitochondrial


Theoretical massNumber of molelcules
Total (without water)384,61738
Polyers384,61738
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)114410
ΔGint (kcal/M)-1309
Surface area (Å2)117730

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Components

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ATP synthase subunit ... , 9 types, 36 molecules 1234567890CDEFGHIJKBaMbNdOePfQ...

#1: Protein/peptide
ATP synthase subunit c, mitochondrial / / Lipid-binding protein / Oligomycin resistance protein 1 / ATP synthase subunit 9 / mitochondrial


Mass: 7762.375 Da / Num. of mol.: 20
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P61829
#3: Protein/peptide ATP synthase subunit a / / F-ATPase protein 6


Mass: 27900.430 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00854
#4: Protein/peptide ATP synthase subunit b /


Mass: 23194.498 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A / References: UniProt: P05626
#5: Protein/peptide ATP synthase subunit d, mitochondrial /


Mass: 19709.424 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P30902
#6: Protein/peptide ATP synthase subunit e, mitochondrial / / ATPase subunit e / Translocase of the inner membrane protein 11


Mass: 4188.154 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#7: Protein/peptide ATP synthase subunit f, mitochondrial /


Mass: 10584.166 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06405
#8: Protein/peptide ATP synthase subunit g /


Mass: 9039.134 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A
#9: Protein/peptide ATP synthase subunit j, mitochondrial / / ATPase synthase I subunit


Mass: 6696.771 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P81450
#10: Protein/peptide ATP synthase subunit k, mitochondrial /


Mass: 7546.778 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P81451

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Protein/peptide , 1 types, 2 molecules AL

#2: Protein/peptide ATP synthase protein 8 / / A6L / ATP-associated protein 1 / F-ATPase subunit 8


Mass: 5825.215 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00856

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast mitochondrial ATP synthase FO complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 / Source: NATURAL
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Cellular location: Inner membrane of mitochondria / Organelle: Mitochondria / Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Homemade
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: blot for 26 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 / Calibrated magnification: 47170 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 71 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 2 / Number of real images: 3023
EM imaging opticsEnergyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
9cryoSPARC0.4.1model refinement
11cryoSPARCfinal Euler assignment
13cryoSPARC0.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 446259
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 238848 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00721828
ELECTRON MICROSCOPYf_angle_d1.07429650
ELECTRON MICROSCOPYf_dihedral_angle_d5.16912690
ELECTRON MICROSCOPYf_chiral_restr0.0543682
ELECTRON MICROSCOPYf_plane_restr0.0083646

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