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- PDB-6zit: bovine ATP synthase Stator domain, state 2 -

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Basic information

Entry
Database: PDB / ID: 6zit
Titlebovine ATP synthase Stator domain, state 2
Components
  • (ATP synthase ...) x 12
  • ATP synthase-coupling factor 6, mitochondrial
KeywordsHYDROLASE / ATP synthase / mitochondria / mammalian / complex
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / 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) / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ADP binding / lipid binding / mitochondrion / ATP 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 F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / 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 / 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 / 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, 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, alpha subunit, C-terminal domain superfamily / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit a / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / 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 a / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / 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: 3.49 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
DepositionJun 26, 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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Structure visualization

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  • Deposited structure unit
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  • EMDB-11229
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Structure viewerMolecule:
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Assembly

Deposited unit
8: ATP synthase protein 8
a: ATP synthase subunit a
d: ATP synthase subunit d, mitochondrial
e: ATP synthase subunit e, mitochondrial
f: ATP synthase subunit f, mitochondrial
g: ATP synthase subunit g, mitochondrial
j: ATP synthase subunit ATP5MPL, mitochondrial
k: ATP synthase membrane subunit DAPIT, mitochondrial
R: ATP synthase F(0) complex subunit C2, mitochondrial
K: ATP synthase F(0) complex subunit C2, mitochondrial
L: ATP synthase F(0) complex subunit C2, mitochondrial
b: ATP synthase F(0) complex subunit B1, mitochondrial
h: ATP synthase-coupling factor 6, mitochondrial
S: ATP synthase subunit O, mitochondrial
C: ATP synthase subunit alpha, mitochondrial


Theoretical massNumber of molelcules
Total (without water)227,10615
Polymers227,10615
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 12 types, 14 molecules 8adefgjkRKLbSC

#1: 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
#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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.: 3 / Source method: isolated from a natural source
Details: Residue 43 is trimethyl-lysine. A post translational modification.
Source: (natural) Bos taurus (cattle) / References: UniProt: P07926
#10: 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
#12: 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
#13: Protein ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55332.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P19483

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Protein , 1 types, 1 molecules h

#11: 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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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 dimeric ATP synthaseCOMPLEXThe imaged sample was intact dimeric ATP synthase. A focussed map was generated for the stator domain.all0MULTIPLE SOURCES
2ATP synthase stator domain, state 2COMPLEXThe stator domain of ATP synthase. 3 c subunits from the rotor domain have been included to define the state.all1NATURAL
3ATP synthase peripheral stalkCOMPLEXMembrane extrinsic part of the stator of the enzyme#3, #10-#131NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.2 MDaYES
210.143 MDaYES
310.0731 MDaYES
41.007441 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (cattle)9913
23Bos taurus (cattle)9913
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
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
4RELION3.1CTF correction
5CTFFIND4.1CTF correction
8Cootmodel fitting
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.17model refinement
15PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.49 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
142WSS

2wss

S1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005310404
ELECTRON MICROSCOPYf_angle_d0.718314063
ELECTRON MICROSCOPYf_chiral_restr0.0421629
ELECTRON MICROSCOPYf_plane_restr0.00551740
ELECTRON MICROSCOPYf_dihedral_angle_d19.58361392

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