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- PDB-6cp5: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhi... -

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Basic information

Entry
Database: PDB / ID: 6cp5
TitleMonomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
Components
  • (ATP synthase subunit ...) x 6
  • ATP synthase protein 8
KeywordsBIOSYNTHETIC PROTEIN / ATP synthase
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
Oligomycin A / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSrivastava, A.P. / Luo, M. / Symersky, J. / Liao, M.F. / Mueller, D.M.
Funding support United States, 1items
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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
K: ATP synthase subunit 9, mitochondrial
L: ATP synthase subunit 9, mitochondrial
M: ATP synthase subunit 9, mitochondrial
N: ATP synthase subunit 9, mitochondrial
O: ATP synthase subunit 9, mitochondrial
P: ATP synthase subunit 9, mitochondrial
Q: ATP synthase subunit 9, mitochondrial
R: ATP synthase subunit 9, mitochondrial
S: ATP synthase subunit 9, mitochondrial
T: ATP synthase subunit 9, mitochondrial
8: ATP synthase protein 8
X: ATP synthase subunit a
Z: ATP synthase subunit 4, mitochondrial
7: ATP synthase subunit d, mitochondrial
U: ATP synthase subunit f, mitochondrial
J: ATP synthase subunit J, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,42820
Polymers169,26316
Non-polymers3,1644
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase subunit ... , 6 types, 15 molecules KLMNOPQRSTXZ7UJ

#1: Protein
ATP synthase subunit 9, mitochondrial / / Lipid-binding protein / Oligomycin resistance protein 1


Mass: 7790.385 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P61829
#3: Protein ATP synthase subunit a / / F-ATPase protein 6


Mass: 27900.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00854
#4: Protein ATP synthase subunit 4, mitochondrial /


Mass: 23194.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05626
#5: Protein ATP synthase subunit d, mitochondrial /


Mass: 19709.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P30902
#6: Protein ATP synthase subunit f, mitochondrial /


Mass: 10584.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06405
#7: Protein/peptide ATP synthase subunit J, mitochondrial / / ATPase synthase I subunit


Mass: 4145.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P81450

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Protein/peptide / Non-polymers , 2 types, 5 molecules 8

#2: Protein/peptide ATP synthase protein 8 / / A6L / ATP-associated protein 1 / F-ATPase subunit 8


Mass: 5825.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00856
#8: Chemical
ChemComp-EFO / Oligomycin A / (1R,4E,5'S,6S,6'S,7R,8S,10R,11R,12S,14R,15S,16R,18E,20E,22R,25S,27R,28S,29R)-22-ethyl-7,11,14,15-tetrahydroxy-6'-[(2R)-2-hydroxypropyl]-5',6,8,10,12,14,16,28,29-nonamethyl-3',4',5',6'-tetrahydro-3H,9H,13H-spiro[2,26-dioxabicyclo[23.3.1]nonacosa-4,18,20-triene-27,2'-pyran]-3,9,13-trione / Oligomycin


Mass: 791.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H74O11 / Comment: antibiotic*YM

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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

ComponentName: Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl, 150 mM NaCl, pH 8.0
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 91 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2700 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 105 K / Temperature (min): 80 K
Image recordingElectron dose: 8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2896

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1SPIDER13particle selection
2RELION1.4particle selection
3UCSFImage44image acquisition
5RELION1.4CTF correction
8Coot0.8.1model fitting
10PHENIX1.11.1model refinement
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 346399
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104280 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039605
ELECTRON MICROSCOPYf_angle_d1.35413036
ELECTRON MICROSCOPYf_dihedral_angle_d5.3265435
ELECTRON MICROSCOPYf_chiral_restr0.1521640
ELECTRON MICROSCOPYf_plane_restr0.0041561

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