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- EMDB-11127: Fo domain of Ovine ATP synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-11127
TitleFo domain of Ovine ATP synthase
Map dataMap of Fo domain, combined states
Sample
  • Complex: Fo domain of purified ATP synthase from sheep heart mitochondria
    • Protein or peptide: x 10 types
  • Ligand: x 3 types
KeywordsATP synthase / mitochondrial / respiratory chain / mammalian / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / proton channel activity / proton-transporting ATP synthase complex / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / : / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane ...: / proton channel activity / proton-transporting ATP synthase complex / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / : / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / lipid binding / mitochondrion
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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 F(0) complex subunit 8 / ATP synthase F(0) complex subunit a / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase membrane subunit K, mitochondrial / Uncharacterized protein / ATP synthase subunit e, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit / ATP synthase subunit f, mitochondrial / ATP synthase subunit b
Similarity search - Component
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsPinke G / Zhou L
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of the entire mammalian F-type ATP synthase.
Authors: Gergely Pinke / Long Zhou / Leonid A Sazanov /
Abstract: The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain ...The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.
History
DepositionJun 5, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6za9
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11127.png

Downloads & links

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Map

FileDownload / File: emd_11127.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of Fo domain, combined states
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 100 pix.
= 106.1 Å		1.06 Å/pix.
x 115 pix.
= 122.015 Å		1.06 Å/pix.
x 122 pix.
= 129.442 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.21077946 - 0.32944193
Average (Standard dev.)0.007973522 (±0.031167299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions115122100
Spacing100115122
CellA: 106.1 Å / B: 122.015 Å / C: 129.442 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z100115122
origin x/y/z0.0000.0000.000
length x/y/z106.100122.015129.442
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS122115100
D min/max/mean-0.2110.3290.008

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Supplemental data

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Sample components

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Entire : Fo domain of purified ATP synthase from sheep heart mitochondria

EntireName: Fo domain of purified ATP synthase from sheep heart mitochondria
Components
  • Complex: Fo domain of purified ATP synthase from sheep heart mitochondria
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase membrane subunit DAPIT
    • Protein or peptide: ATP synthase membrane subunit 6.8PL
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase membrane subunit f
    • Protein or peptide: ATP synthase subunit
    • Protein or peptide: ATP synthase subunit e, mitochondrial
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CARDIOLIPIN
  • Ligand: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine

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Supramolecule #1: Fo domain of purified ATP synthase from sheep heart mitochondria

SupramoleculeName: Fo domain of purified ATP synthase from sheep heart mitochondria
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Ovis aries (sheep)

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Macromolecule #1: ATP synthase F(0) complex subunit C1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 14.201577 KDa
SequenceString:
MQTTGALLIS PALIRSCTRG LIRPVSASFL SRPEIPSVQP SYSSGPLQVA RREFQTSVVS RDIDTAAKFI GAGAATVGVA GSGAGIGTV FGSLIIGYAR NPSLKQQLFS YAILGFALSE AMGLFCLMVA FLILFAM

UniProtKB: ATP synthase F(0) complex subunit C1, mitochondrial

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Macromolecule #2: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 2 / Details: XP_004002367.2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 28.84457 KDa
SequenceString: MLSRVVLSAA AAAAPSLKNA AFLGPGVLQA TRIFHTGQPS LAPVPPLPEH GGKVRFGLIP EEFFQFLYPK TGVTGPYVLG TGLILYLLS KEIYVITPET FSAISTIGFL VYVVKKYGAS VGEFADKLNE QKIAQLEEVK QASIKQIQDA IDMEKSQQAL V QKRHYLFD ...String:
MLSRVVLSAA AAAAPSLKNA AFLGPGVLQA TRIFHTGQPS LAPVPPLPEH GGKVRFGLIP EEFFQFLYPK TGVTGPYVLG TGLILYLLS KEIYVITPET FSAISTIGFL VYVVKKYGAS VGEFADKLNE QKIAQLEEVK QASIKQIQDA IDMEKSQQAL V QKRHYLFD VQRNNIAMAL EVTYRERLHR VYREVKNRLD YHISVQNMMR QKEQEHMINW VEKHVVQSIS AQQEKETIAK CI ADLKLLA KKAQAQPVM

UniProtKB: ATP synthase subunit b

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Macromolecule #3: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 18.747508 KDa
SequenceString:
MAGRKLALKT IDWVAFGEII PRNQKAVANS LKSWNETLTS RLATLPEKPP AIDWAYYKAN VTKAGLVDDF EKKFNALKVP IPEDKYTAQ VDAEEKEDVK SCAEFLIQSK TRIQEYEKEL EKMRNIIPFD QMTIEDLNEV FPETKLDKKK YPYWPHRPIE S L

UniProtKB: ATP synthase subunit d, mitochondrial

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Macromolecule #4: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 24.81185 KDa
SequenceString: MNENLFASFI TPMMFGLPLV TLIVLFPSLL FPTSNRLVNN RLISLQQWML QLVSKQMMSI HNTKGQTWAL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW GGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPVALAVR L TANITAGH ...String:
MNENLFASFI TPMMFGLPLV TLIVLFPSLL FPTSNRLVNN RLISLQQWML QLVSKQMMSI HNTKGQTWAL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW GGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPVALAVR L TANITAGH LLIHLIGGAT LALMSINTTT ALITFIILIL LTVLEFAVAM IQAYVFTLLV SLYLHDNT

UniProtKB: ATP synthase F(0) complex subunit a

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Macromolecule #5: ATP synthase membrane subunit DAPIT

MacromoleculeName: ATP synthase membrane subunit DAPIT / type: protein_or_peptide / ID: 5 / Details: ATP synthase membrane subunit DAPIT / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 6.443579 KDa
SequenceString:
MAGPEADAQF HFTGIKKYFN SYTLTGRMNC VLATYGSIAL IVLYFKLRSK KTPAVKAT

UniProtKB: ATP synthase membrane subunit K, mitochondrial

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Macromolecule #6: ATP synthase membrane subunit 6.8PL

MacromoleculeName: ATP synthase membrane subunit 6.8PL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 6.846093 KDa
SequenceString:
MLQSLIKKVW IPMKPYYTQA YQEIWVGTGL MAYIVYKIRS ADKRSKALKA SSAAPAHGHH

UniProtKB: Uncharacterized protein

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Macromolecule #7: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 7.918443 KDa
SequenceString:
MPQLDTSTWL TMILSMFLVL FIIFQLKISK HNFYHNPELM TTKTPKQNTP WETKWTKIYL PLSLPL

UniProtKB: ATP synthase F(0) complex subunit 8

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Macromolecule #8: ATP synthase membrane subunit f

MacromoleculeName: ATP synthase membrane subunit f / type: protein_or_peptide / ID: 8 / Details: ATP synthase subunit f, XP_004016938.3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 10.315207 KDa
SequenceString:
MASVVPLKEK KLLEVKLGEL PSWILMRDFT PSGIAGAFQR GYYRYYNKYV NVKKGSIAGL SMVLAAYVFL NYCRSYKELK HERLRKYH

UniProtKB: ATP synthase subunit f, mitochondrial

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Macromolecule #9: ATP synthase subunit

MacromoleculeName: ATP synthase subunit / type: protein_or_peptide / ID: 9 / Details: XP_011950914.1, ATP synthase subunit g / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 11.428407 KDa
SequenceString:
MAQFVRNLAE KAPALVNAAV TYSKPRLATF WYYAKVELVP PTPAEIPTAI QSLKKIINSA KTGSFKQLTV KEALLNGLVA TEVWMWFYV GEIIGKRGII GYDV

UniProtKB: ATP synthase subunit

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Macromolecule #10: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 10 / Details: XP_027827162.1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 8.336688 KDa
SequenceString:
MVPPVQVSPL IKLGRYSALF LGMAYGAKRY NYLKPRAEEE RRLAAEEKKK RDEQKRIERE LAEAQEDTIL K

UniProtKB: ATP synthase subunit e, mitochondrial

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Macromolecule #11: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 11 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #12: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 12 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #13: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}p...

MacromoleculeName: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
type: ligand / ID: 13 / Number of copies: 1 / Formula: S12
Molecular weightTheoretical: 523.597 Da
Chemical component information

ChemComp-S12:
O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine

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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

Concentration2.8 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES pH7.4, 35 mM NaCl, 2 mM EDTA, 1% sucrose, 1 mM DTT, 0.1% LMNG, 0.2% CHAPS
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3053 / Average exposure time: 1.0 sec. / Average electron dose: 106.0 e/Å2 / Details: 40 frames per movie
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.4 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 131951 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 809000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ara

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 217266
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ara


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 77
Output model

PDB-6za9:
Fo domain of Ovine ATP synthase

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