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- EMDB-11149: bovine ATP synthase Fo domain -

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Basic information

Entry
Database: EMDB / ID: EMD-11149
Titlebovine ATP synthase Fo domain
Map dataFo main map
Sample
  • Complex: ATP synthase
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
Function / homology
Function and homology information


Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, stator stalk / 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 ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, stator stalk / 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 / lipid binding
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
ATP synthase subunit a / ATP synthase protein 8 / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase F(0) complex subunit C1, 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) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsSpikes T / Montgomery MG / Walker JE
Funding support United Kingdom, 2 items
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 8, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0197
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0197
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zbb
  • Surface level: 0.0197
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11149.png

Downloads & links

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Map

FileDownload / File: emd_11149.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFo main map
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 0.0197 / Movie #1: 0.0197
Minimum - Maximum-0.040173244 - 0.08055188
Average (Standard dev.)-0.0000669159 (±0.001206267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 524.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z524.000524.000524.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0400.081-0.000

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Supplemental data

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Mask #1

Fileemd_11149_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Fo half map 1

Fileemd_11149_half_map_1.map
AnnotationFo half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Fo half map 2

Fileemd_11149_half_map_2.map
AnnotationFo half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATP synthase

EntireName: ATP synthase
Components
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase F(0) complex subunit B1, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit e, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit g, mitochondrial
    • Protein or peptide: ATP synthase subunit ATP5MPL, mitochondrial
    • Protein or peptide: ATP synthase membrane subunit DAPIT, mitochondrial
  • Ligand: CARDIOLIPIN
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 / Details: dimeric ATP synthase was the imaged sample.
Source (natural)Organism: Bos taurus (cattle)
Molecular weightExperimental: 7.441 KDa

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Macromolecule #1: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 7.944523 KDa
SequenceString:
MPQLDTSTWL TMILSMFLTL FIIFQLKVSK HNFYHNPELT PTKMLKQNTP WETKWTKIYL PLLLPL

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Macromolecule #2: ATP synthase F(0) complex subunit C1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C1, mitochondrial / type: protein_or_peptide / ID: 2
Details: Residue 43 is tri-methyl lysine. A post translational modification.
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 7.653034 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SL(M3L)QQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM

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Macromolecule #3: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 24.801785 KDa
SequenceString: MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW AGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPMALAVR L TANITAGH ...String:
MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW AGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPMALAVR L TANITAGH LLIHLIGGAT LALMSISTTT ALITFTILIL LTILEFAVAM IQAYVFTLLV SLYLHDNT

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Macromolecule #4: ATP synthase F(0) complex subunit B1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 24.702709 KDa
SequenceString: PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYR EVKNRLDYHI S VQNMMRQK ...String:
PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYR EVKNRLDYHI S VQNMMRQK EQEHMINWVE KRVVQSISAQ QEKETIAKCI ADLKLLSKKA QAQPVM

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Macromolecule #5: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 18.588256 KDa
SequenceString:
AGRKLALKTI DWVAFGEIIP RNQKAVANSL KSWNETLTSR LATLPEKPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPI PEDKYTAQV DAEEKEDVKS CAEFLTQSKT RIQEYEKELE KMRNIIPFDQ MTIEDLNEVF PETKLDKKKY PYWPHRPIET L

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Macromolecule #6: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 8.205492 KDa
SequenceString:
VPPVQVSPLI KLGRYSALFL GMAYGAKRYN YLKPRAEEER RLAAEEKKKR DEQKRIEREL AEAQEDTILK

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Macromolecule #7: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 10.184011 KDa
SequenceString:
ASVVPLKEKK LLEVKLGELP SWILMRDFTP SGIAGAFQRG YYRYYNKYVN VKKGSIAGLS MVLAAYVFLN YCRSYKELKH ERLRKYH

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Macromolecule #8: ATP synthase subunit g, mitochondrial

MacromoleculeName: ATP synthase subunit g, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 11.298196 KDa
SequenceString:
AEFVRNLAEK APALVNAAVT YSKPRLATFW YYAKVELVPP TPAEIPTAIQ SLKKIINSAK TGSFKQLTVK EALLNGLVAT EVWMWFYVG EIIGKRGIIG YDV

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Macromolecule #9: ATP synthase subunit ATP5MPL, mitochondrial

MacromoleculeName: ATP synthase subunit ATP5MPL, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 6.846093 KDa
SequenceString:
MLQSLIKKVW IPMKPYYTQA YQEIWVGTGL MAYIVYKIRS ADKRSKALKA SSAAPAHGHH

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Macromolecule #10: ATP synthase membrane subunit DAPIT, mitochondrial

MacromoleculeName: ATP synthase membrane subunit DAPIT, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 6.312383 KDa
SequenceString:
AGPEADAQFH FTGIKKYFNS YTLTGRMNCV LATYGSIALI VLYFKLRSKK TPAVKAT

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Macromolecule #11: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 11 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #12: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 12 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV
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..
DetailsNickel affinity purified filled by gel filtration

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 4.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: RELION (ver. 3.1), CTFFIND (ver. 4.1))
Startup model#0 - Type of model: PDB ENTRY
#0 - PDB model - PDB ID:

2xnd


#1 - Type of model: PDB ENTRY
#1 - PDB model - PDB ID:

5ara

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 253473
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

5ara

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2xnd

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6zbb:
bovine ATP synthase Fo domain

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