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- PDB-6zna: Porcine ATP synthase Fo domain -

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Basic information

Entry
Database: PDB / ID: 6zna
TitlePorcine ATP synthase Fo domain
Components(ATP synthase ...) x 10
KeywordsHYDROLASE / mitochondrion / ATP synthase / porcine / complex
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / ubiquitin-ubiquitin ligase activity / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / : ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / ubiquitin-ubiquitin ligase activity / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / : / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / protein polyubiquitination / lipid binding / mitochondrion / membrane / nucleus / cytoplasm
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
CARDIOLIPIN / ATP synthase subunit b / ATP synthase subunit d, mitochondrial / ATP synthase membrane subunit 6.8PL / ATP synthase membrane subunit K, mitochondrial / ATP synthase lipid-binding protein / ATP synthase subunit / ATP synthase protein 8 / ATP synthase subunit a / ATP synthase subunit f, mitochondrial / ATP synthase subunit e, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsSpikes, T.E. / Montgomery, M.G. / Walker, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the dimeric ATP synthase from bovine mitochondria.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
History
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A8: ATP synthase protein 8
AK: ATP synthase F(0) complex subunit C1, mitochondrial
AL: ATP synthase F(0) complex subunit C1, mitochondrial
AM: ATP synthase F(0) complex subunit C1, mitochondrial
AN: ATP synthase F(0) complex subunit C1, mitochondrial
AO: ATP synthase F(0) complex subunit C1, mitochondrial
AP: ATP synthase F(0) complex subunit C1, mitochondrial
AQ: ATP synthase F(0) complex subunit C1, mitochondrial
AR: ATP synthase F(0) complex subunit C1, mitochondrial
Aa: ATP synthase subunit a
Ab: ATP synthase peripheral stalk-membrane subunit b
Ad: ATP synthase subunit d, mitochondrial
Ae: ATP synthase subunit e, mitochondrial
Af: ATP synthase subunit f, mitochondrial
Ag: ATP synthase g subunit
Aj: ATP synthase j subunit (6.8PL)
Ak: ATP synthase membrane subunit DAPIT
B8: ATP synthase protein 8
BK: ATP synthase F(0) complex subunit C1, mitochondrial
BL: ATP synthase F(0) complex subunit C1, mitochondrial
BM: ATP synthase F(0) complex subunit C1, mitochondrial
BN: ATP synthase F(0) complex subunit C1, mitochondrial
BO: ATP synthase F(0) complex subunit C1, mitochondrial
BP: ATP synthase F(0) complex subunit C1, mitochondrial
BQ: ATP synthase F(0) complex subunit C1, mitochondrial
BR: ATP synthase F(0) complex subunit C1, mitochondrial
Ba: ATP synthase subunit a
Bb: ATP synthase peripheral stalk-membrane subunit b
Bd: ATP synthase subunit d, mitochondrial
Be: ATP synthase subunit e, mitochondrial
Bf: ATP synthase subunit f, mitochondrial
Bg: ATP synthase g subunit
Bj: ATP synthase j subunit (6.8PL)
Bk: ATP synthase membrane subunit DAPIT
C8: ATP synthase protein 8
CK: ATP synthase F(0) complex subunit C1, mitochondrial
CL: ATP synthase F(0) complex subunit C1, mitochondrial
CM: ATP synthase F(0) complex subunit C1, mitochondrial
CN: ATP synthase F(0) complex subunit C1, mitochondrial
CO: ATP synthase F(0) complex subunit C1, mitochondrial
CP: ATP synthase F(0) complex subunit C1, mitochondrial
CQ: ATP synthase F(0) complex subunit C1, mitochondrial
CR: ATP synthase F(0) complex subunit C1, mitochondrial
Ca: ATP synthase subunit a
Cb: ATP synthase peripheral stalk-membrane subunit b
Cd: ATP synthase subunit d, mitochondrial
Ce: ATP synthase subunit e, mitochondrial
Cf: ATP synthase subunit f, mitochondrial
Cg: ATP synthase g subunit
Cj: ATP synthase j subunit (6.8PL)
Ck: ATP synthase membrane subunit DAPIT
K: ATP synthase F(0) complex subunit C1, mitochondrial
L: ATP synthase F(0) complex subunit C1, mitochondrial
M: ATP synthase F(0) complex subunit C1, mitochondrial
N: ATP synthase F(0) complex subunit C1, mitochondrial
O: ATP synthase F(0) complex subunit C1, mitochondrial
P: ATP synthase F(0) complex subunit C1, mitochondrial
Q: ATP synthase F(0) complex subunit C1, mitochondrial
R: ATP synthase F(0) complex subunit C1, mitochondrial
a: ATP synthase subunit a
b: ATP synthase peripheral stalk-membrane subunit b
d: ATP synthase subunit d, mitochondrial
e: ATP synthase subunit e, mitochondrial
f: ATP synthase subunit f, mitochondrial
g: ATP synthase g subunit
8: ATP synthase protein 8
j: ATP synthase j subunit (6.8PL)
k: ATP synthase membrane subunit DAPIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)725,19072
Polymers719,33468
Non-polymers5,8564
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area76700 Å2
ΔGint-886 kcal/mol
Surface area268680 Å2
MethodPISA

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Components

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ATP synthase ... , 10 types, 68 molecules A8B8C88AKALAMANAOAPAQARBKBLBMBNBOBPBQBRCKCLCMCNCOCPCQCRKL...

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


Mass: 7954.407 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35914
#2: Protein ...
ATP synthase F(0) complex subunit C1, mitochondrial


Mass: 7653.034 Da / Num. of mol.: 32 / Source method: isolated from a natural source
Details: Residue 43 is trimethyl-lysine. A postranslational modification.
Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWF6
#3: Protein
ATP synthase subunit a / / F-ATPase protein 6


Mass: 25054.143 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35915
#4: Protein
ATP synthase peripheral stalk-membrane subunit b


Mass: 24508.584 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZYM6
#5: Protein
ATP synthase subunit d, mitochondrial /


Mass: 18411.186 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287A2Y4
#6: Protein
ATP synthase subunit e, mitochondrial / / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8115.364 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9MYT8
#7: Protein
ATP synthase subunit f, mitochondrial / / ATP synthase membrane subunit f


Mass: 10197.959 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q95339
#8: Protein
ATP synthase g subunit / ATP synthase g subunit


Mass: 11198.080 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ATP synthase g subunit / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAK7
#9: Protein
ATP synthase j subunit (6.8PL) / ATP synthase j subunit (6.8PL)


Mass: 6867.134 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ATP synthase j subunit (6.8PL) / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TX70
#10: Protein
ATP synthase membrane subunit DAPIT


Mass: 6302.365 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RFD4

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Non-polymers , 1 types, 4 molecules

#11: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*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: Porcine ATP synthase Fo domain / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170000 / Symmetry type: POINT

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