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- PDB-6j54: Cryo-EM structure of the mammalian E-state ATP synthase FO section -

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Basic information

Entry
Database: PDB / ID: 6j54
TitleCryo-EM structure of the mammalian E-state ATP synthase FO section
Components
  • (ATP synthase ...) x 9
  • Mitochondrial H+ transporting ATP synthase subunit c isoform 1
  • subunit k analog
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / 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 ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / 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 / mitochondrial membrane / lipid binding
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / F1F0 ATP synthase subunit C / F1FO ATP Synthase / 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 membrane subunit K / ATP synthase regulation / F1F0 ATP synthase subunit C / F1FO ATP Synthase / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase subunit b / ATP synthase subunit d, mitochondrial / ATP synthase membrane subunit K, mitochondrial / ATP synthase protein 8 / ATP synthase subunit a / ATP synthase lipid-binding protein / ATP synthase subunit f, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsGu, J. / Zhang, L. / Yi, J. / Yang, M.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0504600 and 2016YFA0501100 China
National Natural Science Foundation of China31625008 China
National Natural Science Foundation of China21532004, 31570733 and 31800620 China
CitationJournal: Science / Year: 2019
Title: Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1.
Authors: Jinke Gu / Laixing Zhang / Shuai Zong / Runyu Guo / Tianya Liu / Jingbo Yi / Peiyi Wang / Wei Zhuo / Maojun Yang /
Abstract: The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom ...The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo-electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
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 subunit g, mitochondrial
i: ATP synthase membrane subunit DAPIT
k: subunit k analog
8: ATP synthase protein 8
a: ATP synthase subunit a
K: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
L: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
M: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
N: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
O: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
P: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
Q: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
R: Mitochondrial H+ transporting ATP synthase subunit c isoform 1
u: ATP synthase membrane subunit 6.8PL


Theoretical massNumber of molelcules
Total (without water)132,62918
Polymers132,62918
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 9 types, 9 molecules bdefgi8au

#1: Protein ATP synthase peripheral stalk-membrane subunit b


Mass: 8886.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZYM6
#2: Protein/peptide ATP synthase subunit d, mitochondrial /


Mass: 2933.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B4I0
#3: Protein ATP synthase subunit e, mitochondrial /


Mass: 5379.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#4: Protein ATP synthase subunit f, mitochondrial / / ATP synthase membrane subunit f


Mass: 10197.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q95339
#5: Protein ATP synthase subunit g, mitochondrial /


Mass: 7166.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#6: Protein/peptide ATP synthase membrane subunit DAPIT


Mass: 4861.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RFD4
#8: Protein/peptide ATP synthase protein 8 / / A6L / F-ATPase subunit 8


Mass: 3577.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35914
#9: Protein ATP synthase subunit a / / F-ATPase protein 6


Mass: 25054.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35915
#11: Protein/peptide ATP synthase membrane subunit 6.8PL


Mass: 3592.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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Protein/peptide / Protein , 2 types, 9 molecules kKLMNOPQR

#10: Protein
Mitochondrial H+ transporting ATP synthase subunit c isoform 1


Mass: 7311.631 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q4VT52
#7: Protein/peptide subunit k analog


Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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Details

Sequence detailsThe sequence of the chain e corresponds to Q03654 in the UniProt database. The sequence of the ...The sequence of the chain e corresponds to Q03654 in the UniProt database. The sequence of the chain g corresponds to A0A480XS10 in the UniProt database. The sequence of the chain u corresponds to F1S9V7 in the UniProt database. However, there are UNK (unknown residues) in these chains, as the authors do not know how the coordinates align with the sequences. Therefore the residues numbers are meaningless. As for k chain, the authors don’t know the reference sequence in the UniProt database.

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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: Cryo-EM structure of the mammalian E-state ATP synthase FO section
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7
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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167954 / Symmetry type: POINT

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