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- EMDB-7547: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhi... -

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Basic information

Entry
Database: EMDB / ID: EMD-7547
TitleMonomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
Map dataMonomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound
Sample
  • Complex: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
    • Protein or peptide: ATP synthase subunit 9, mitochondrial
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit 4, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit J, mitochondrial
  • Ligand: Oligomycin A
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex assembly / 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 ATP synthesis / proton transmembrane transporter activity / proton transmembrane transport / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane ...mitochondrial proton-transporting ATP synthase complex assembly / 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 ATP synthesis / proton transmembrane transporter activity / proton transmembrane transport / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / mitochondrion / identical protein binding / cytosol
Similarity search - Function
ATP synthase, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / 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, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / 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 subunit 4, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit f, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSrivastava AP / Luo M / Symersky J / Liao MF / Mueller DM
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)R01GM66223 United States
CitationJournal: Science / Year: 2018
Title: High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane.
Authors: Anurag P Srivastava / Min Luo / Wenchang Zhou / Jindrich Symersky / Dongyang Bai / Melissa G Chambers / José D Faraldo-Gómez / Maofu Liao / David M Mueller /
Abstract: Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F motor that rotates to drive ATP synthesis in the F subunit. We used single-particle cryo-electron microscopy (cryo- ...Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F motor that rotates to drive ATP synthesis in the F subunit. We used single-particle cryo-electron microscopy (cryo-EM) to obtain structures of the full complex in a lipid bilayer in the absence or presence of the inhibitor oligomycin at 3.6- and 3.8-angstrom resolution, respectively. To limit conformational heterogeneity, we locked the rotor in a single conformation by fusing the F6 subunit of the stator with the δ subunit of the rotor. Assembly of the enzyme with the F6-δ fusion caused a twisting of the rotor and a 9° rotation of the F c-ring in the direction of ATP synthesis, relative to the structure of isolated F Our cryo-EM structures show how F and F are coupled, give insight into the proton translocation pathway, and show how oligomycin blocks ATP synthesis.
History
DepositionMar 13, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 11, 2018-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cp5
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7547.png

Downloads & links

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Map

FileDownload / File: emd_7547.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy EMDB: 0.0445 / Movie #1: 0.045
Minimum - Maximum-0.10081425 - 0.1641256
Average (Standard dev.)0.0000005772 (±0.005015565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.1010.1640.000

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Supplemental data

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Supplemental map: emd 7547 additional.map

Fileemd_7547_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhi...

EntireName: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
Components
  • Complex: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
    • Protein or peptide: ATP synthase subunit 9, mitochondrial
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit 4, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit J, mitochondrial
  • Ligand: Oligomycin A

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Supramolecule #1: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhi...

SupramoleculeName: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c

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Macromolecule #1: ATP synthase subunit 9, mitochondrial

MacromoleculeName: ATP synthase subunit 9, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.790385 KDa
SequenceString:
(FME)QLVLAAKYI GAGISTIGLL GAGIGIAIVF AALINGVSRN PSIKDTVFPM AILGFALSEA TGLFCLMVSF LLLFGV

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Macromolecule #2: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.825215 KDa
SequenceString:
MPQLVPFYFM NQLTYGFLLM ITLLILFSQF FLPMILRLYV SRLFISKL

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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: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.90043 KDa
SequenceString: SPLDQFEIRT LFGLQSSFID LSCLNLTTFS LYTIIVLLVI TSLYTLTNNN NKIIGSRWLI SQEAIYDTIM NMTKGQIGGK NWGLYFPMI FTLFMFIFIA NLISMIPYSF ALSAHLVFII SLSIVIWLGN TILGLYKHGW VFFSLFVPAG TPLPLVPLLV I IETLSYFA ...String:
SPLDQFEIRT LFGLQSSFID LSCLNLTTFS LYTIIVLLVI TSLYTLTNNN NKIIGSRWLI SQEAIYDTIM NMTKGQIGGK NWGLYFPMI FTLFMFIFIA NLISMIPYSF ALSAHLVFII SLSIVIWLGN TILGLYKHGW VFFSLFVPAG TPLPLVPLLV I IETLSYFA RAISLGLRLG SNILAGHLLM VILAGLTFNF MLINLFTLVF GFVPLAMILA IMMLEFAIGI IQGYVWAILT AS YLKDAVY LH

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Macromolecule #4: ATP synthase subunit 4, mitochondrial

MacromoleculeName: ATP synthase subunit 4, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 23.194498 KDa
SequenceString: MSSTPEKQTD PKAKANSIIN AIPGNNILTK TGVLGTSAAA VIYAISNELY VINDESILLL TFLGFTGLVA KYLAPAYKDF ADARMKKVS DVLNASRNKH VEAVKDRIDS VSQLQNVAET TKVLFDVSKE TVELESEAFE LKQKVELAHE AKAVLDSWVR Y EASLRQLE ...String:
MSSTPEKQTD PKAKANSIIN AIPGNNILTK TGVLGTSAAA VIYAISNELY VINDESILLL TFLGFTGLVA KYLAPAYKDF ADARMKKVS DVLNASRNKH VEAVKDRIDS VSQLQNVAET TKVLFDVSKE TVELESEAFE LKQKVELAHE AKAVLDSWVR Y EASLRQLE QRQLAKSVIS RVQSELGNPK FQEKVLQQSI SEIEQLLSKL K

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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: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 19.709424 KDa
SequenceString:
SLAKSAANKL DWAKVISSLR ITGSTATQLS SFKKRNDEAR RQLLELQSQP TEVDFSHYRS VLKNTSVIDK IESYVKQYKP VKIDASKQL QVIESFEKHA MTNAKETESL VSKELKDLQS TLDNIQSARP FDELTVDDLT KIKPEIDAKV EEMVKKGKWD V PGYKDRFG NLNVM

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Macromolecule #6: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.584166 KDa
SequenceString:
VSTLIPPKVV SSKNIGSAPN AKRIANVVHF YKSLPQGPAP AIKANTRLAR YKAKYFDGDN ASGKPLWHFA LGIIAFGYSM EYYFHLRHH KGAEEH

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Macromolecule #7: ATP synthase subunit J, mitochondrial

MacromoleculeName: ATP synthase subunit J, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.145884 KDa
SequenceString:
MLKRFPTPIL KVYWPFFVAG AAVYYGMSKA ADLSSNT

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Macromolecule #8: Oligomycin A

MacromoleculeName: Oligomycin A / type: ligand / ID: 8 / Number of copies: 4 / Formula: EFO
Molecular weightTheoretical: 791.062 Da
Chemical component information

ChemComp-EFO:
Oligomycin A / antibiotic*YM / Oligomycin

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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

Concentration1.0 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 150 mM NaCl, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 91 %

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.7 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 105.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2896 / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 346399
CTF correctionSoftware - Name: RELION (ver. 1.4)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 104280
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6cp5:
Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.

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