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- EMDB-7549: Monomer yeast ATP synthase Fo reconstituted in nanodisc generated... -

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Basic information

Entry
Database: EMDB / ID: EMD-7549
TitleMonomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement.
Map dataMonomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement
Sample
  • Complex: Monomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked 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
KeywordsATP synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton transmembrane transport / mitochondrial intermembrane space / protein-containing complex assembly ...Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / 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) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsSrivastava AP / Luo M
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) releaseMar 28, 2018-
Map releaseApr 11, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0475
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0475
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cp7
  • Surface level: 0.0475
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7549.png

Downloads & links

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Map

FileDownload / File: emd_7549.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0475 / Movie #1: 0.0475
Minimum - Maximum-0.1009411 - 0.18003838
Average (Standard dev.)-0.000004271491 (±0.006341688)
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-0.1010.180-0.000

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Supplemental data

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Supplemental map: emd 7549 additional.map

Fileemd_7549_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 generated...

EntireName: Monomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement.
Components
  • Complex: Monomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked 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

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

SupramoleculeName: Monomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.790385 KDa
SequenceString:
(FME)QLVLAAKYI GAGISTIGLL GAGIGIAIVF AALINGVSRN PSIKDTVFPM AILGFALSEA TGLFCLMVSF LLLFGV

UniProtKB: ATP synthase subunit 9, mitochondrial

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.825215 KDa
SequenceString:
MPQLVPFYFM NQLTYGFLLM ITLLILFSQF FLPMILRLYV SRLFISKL

UniProtKB: ATP synthase protein 8

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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

UniProtKB: ATP synthase subunit a

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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

UniProtKB: ATP synthase subunit 4, mitochondrial

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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

UniProtKB: ATP synthase subunit d, mitochondrial

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.584166 KDa
SequenceString:
VSTLIPPKVV SSKNIGSAPN AKRIANVVHF YKSLPQGPAP AIKANTRLAR YKAKYFDGDN ASGKPLWHFA LGIIAFGYSM EYYFHLRHH KGAEEH

UniProtKB: ATP synthase subunit f, mitochondrial

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.145884 KDa
SequenceString:
MLKRFPTPIL KVYWPFFVAG AAVYYGMSKA ADLSSNT

UniProtKB: ATP synthase subunit J, mitochondrial

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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. 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 / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 91 %

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Electron microscopy

MicroscopeFEI POLARA 300
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: 5935 / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.6 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 541568
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 109206
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6cp7:
Monomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement.

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