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- PDB-6yo0: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -

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Basic information

Entry
Database: PDB / ID: 6yo0
TitleCryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1/peripheral stalk
Components
  • (ATP synthase subunit ...) x 3
  • ATPTT13
  • Inhibitor of F1 (IF1)
  • Oligomycin sensitivity-conferring protein (OSCP)
  • subunit b
  • subunit d
KeywordsMEMBRANE PROTEIN / mitochondria / ATP synthase / F1-subcomplex / peripheral stalk / IF1
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily ...ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / ATP synthase F1, delta subunit / ATP synthase subunit gamma / Uncharacterized protein / ATP synthase subunit alpha
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKock Flygaard, R. / Muhleip, A. / Amunts, A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
CitationJournal: Nat Commun / Year: 2020
Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts /
Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
G1: Oligomycin sensitivity-conferring protein (OSCP)
g1: ATP synthase subunit gamma
C1: ATP synthase subunit alpha
D1: ATP synthase subunit beta
B1: ATP synthase subunit alpha
F1: ATP synthase subunit beta
A1: ATP synthase subunit alpha
E1: ATP synthase subunit beta
i1: Inhibitor of F1 (IF1)
s: ATPTT13
b: subunit b
d: subunit d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,36222
Polymers497,86412
Non-polymers2,49710
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area57190 Å2
ΔGint-348 kcal/mol
Surface area131850 Å2
MethodPISA

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Components

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Protein , 5 types, 5 molecules G1i1sbd

#1: Protein Oligomycin sensitivity-conferring protein (OSCP)


Mass: 24782.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MMI7
#5: Protein Inhibitor of F1 (IF1)


Mass: 12987.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M7C0
#6: Protein ATPTT13


Mass: 16816.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLU7
#7: Protein subunit b


Mass: 43910.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MJ84
#8: Protein subunit d


Mass: 26747.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q239R1

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ATP synthase subunit ... , 3 types, 7 molecules g1C1B1A1D1F1E1

#2: Protein ATP synthase subunit gamma /


Mass: 32915.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22Z05
#3: Protein ATP synthase subunit alpha /


Mass: 59744.012 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24HY8
#4: Protein ATP synthase subunit beta /


Mass: 53490.848 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LZV1

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Non-polymers , 3 types, 10 molecules

#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial ATP synthase, F1/peripheral stalk / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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: 165000 X
Image recordingElectron dose: 30.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.1particle selectionbeta
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
10RELION3.1initial Euler assignmentbeta
11RELION3.1final Euler assignmentbeta
13RELION3.13D reconstructionbeta
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61157 / Symmetry type: POINT

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