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- PDB-6zqm: bovine ATP synthase monomer state 2 (combined) -

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Basic information

Entry
Database: PDB / ID: 6zqm
Titlebovine ATP synthase monomer state 2 (combined)
Components
  • (ATP synthase ...) x 16
  • ATP synthase-coupling factor 6, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsHYDROLASE / ATP synthase / mitochondria / mammalian / complex
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / : / : ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / : / : / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial 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 / aerobic respiration / proton transmembrane transport / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane
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 ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial ATPase inhibitor, IATP / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / 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. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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 / CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / ATP synthase subunit delta, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit e, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase membrane subunit K, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSpikes, T.E. / Montgomery, M.G. / Walker, J.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105663150 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 10, 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
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
K: ATP synthase F(0) complex subunit C2, mitochondrial
L: ATP synthase F(0) complex subunit C2, mitochondrial
M: ATP synthase F(0) complex subunit C2, mitochondrial
N: ATP synthase F(0) complex subunit C2, mitochondrial
O: ATP synthase F(0) complex subunit C2, mitochondrial
P: ATP synthase F(0) complex subunit C2, mitochondrial
Q: ATP synthase F(0) complex subunit C2, mitochondrial
R: ATP synthase F(0) complex subunit C2, mitochondrial
S: ATP synthase subunit O, mitochondrial
8: ATP synthase protein 8
a: ATP synthase subunit a
d: ATP synthase subunit d, mitochondrial
f: ATP synthase subunit f, mitochondrial
g: ATP synthase subunit g, mitochondrial
j: ATP synthase subunit ATP5MPL, mitochondrial
b: ATP synthase F(0) complex subunit B1, mitochondrial
h: ATP synthase-coupling factor 6, mitochondrial
k: ATP synthase membrane subunit DAPIT, mitochondrial
e: ATP synthase subunit e, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,48245
Polymers589,71929
Non-polymers8,76316
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area121630 Å2
ΔGint-960 kcal/mol
Surface area190520 Å2
MethodPISA

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Components

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ATP synthase ... , 16 types, 27 molecules ABCDEFGHIKLMNOPQRS8adfgjbke

#1: Protein ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55302.191 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P19483
#2: Protein ATP synthase subunit beta, mitochondrial


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma, mitochondrial / F-ATPase gamma subunit


Mass: 30300.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05631
#4: Protein ATP synthase subunit delta, mitochondrial / F-ATPase delta subunit


Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05630
#5: Protein/peptide ATP synthase subunit epsilon, mitochondrial / ATPase subunit epsilon


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P05632
#7: Protein
ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase proteolipid P2 / ATPase protein 9 / ATPase subunit c


Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: Residue 43 is trimethyl-lysine. A postranslational modification.
Source: (natural) Bos taurus (cattle) / References: UniProt: P07926
#8: Protein ATP synthase subunit O, mitochondrial / ATP synthase peripheral stalk subunit OSCP / Oligomycin sensitivity conferral protein / OSCP


Mass: 20959.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13621
#9: Protein ATP synthase protein 8 / A6L / F-ATPase subunit 8


Mass: 7944.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P03929
#10: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 24801.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00847
#11: Protein ATP synthase subunit d, mitochondrial / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18588.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13620
#12: Protein ATP synthase subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 10184.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28851
#13: Protein ATP synthase subunit g, mitochondrial / ATPase subunit g / ATP synthase membrane subunit g


Mass: 11298.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28852
#14: Protein ATP synthase subunit ATP5MPL, mitochondrial / 6.8 kDa mitochondrial proteolipid / 6.8 kDa mitochondrial proteolipid protein / MLQ


Mass: 6846.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P14790
#15: Protein ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 24702.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13619
#17: Protein ATP synthase membrane subunit DAPIT, mitochondrial / Diabetes-associated protein in insulin-sensitive tissues / Up-regulated during skeletal muscle ...Diabetes-associated protein in insulin-sensitive tissues / Up-regulated during skeletal muscle growth protein 5


Mass: 6312.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZBI7
#18: Protein ATP synthase subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8205.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q00361

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Protein , 2 types, 2 molecules Jh

#6: Protein ATPase inhibitor, mitochondrial / Inhibitor of F(1)F(o)-ATPase / IF1


Mass: 7462.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ATP synthase inhibitor protein IF1 residues 1-60 with a 6His tag
Source: (gene. exp.) Bos taurus (cattle) / Gene: ATPIF1, ATPI / Production host: Escherichia coli (E. coli) / References: UniProt: P01096
#16: Protein ATP synthase-coupling factor 6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 8971.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02721

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Non-polymers , 6 types, 33 molecules

#19: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


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


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#22: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#23: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#24: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Bovine ATP synthaseCOMPLEXbovine ATP synthase inhibited by IF1 1-60His#1-#180MULTIPLE SOURCES
2monomeric bovine ATP synthase, state 2COMPLEXmonomeric bovine ATP synthase inhibited by IF1 1-60His, state 2#1-#5, #7-#181NATURAL
3Bovine ATP synthaseCOMPLEX#61RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.2 MDaYES
210.6 MDaYES
310.0731 MDaYES
410.007441 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (cattle)9913
23Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Nickel affinity purified filled by gel filtration
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K
Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting.

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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 FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 4.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3922refinement
PHENIXdev_3922refinement
EM software
IDNameVersionCategory
4RELION3.1CTF correction
5CTFFIND4.1CTF correction
10PHENIX1.17model refinement
11PHENIX1.18model refinement
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90850 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
12V7Q

2v7q

A1
22V7Q

2v7q

B1
32V7Q

2v7q

C1
42V7Q

2v7q

D1
52V7Q

2v7q

E1
62V7Q

2v7q

F1
72V7Q

2v7q

G1
82V7Q

2v7q

H1
92V7Q

2v7q

I1
102V7Q

2v7q

J1
112CLY

2cly

A1
122CLY

2cly

B1
132CLY

2cly

C1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 38.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008740625
ELECTRON MICROSCOPYf_angle_d0.717154883
ELECTRON MICROSCOPYf_chiral_restr0.04666353
ELECTRON MICROSCOPYf_plane_restr0.00416942
ELECTRON MICROSCOPYf_dihedral_angle_d16.82015872

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