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- PDB-6cp3: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with ... -

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Basic information

Entry
Database: PDB / ID: 6cp3
TitleMonomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
Components
  • (ATP synthase subunit ...) x 13
  • ATP synthase protein 8
KeywordsBIOSYNTHETIC PROTEIN / ATP synthase
Function / homology
Function and homology information


cristae formation / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase ...cristae formation / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ADP binding / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / N-terminal domain of the delta subunit of the F1F0-ATP synthase / ATP synthase, F0 complex, subunit H / ATP synthase complex subunit h / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / ATP synthase, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / N-terminal domain of the delta subunit of the F1F0-ATP synthase / ATP synthase, F0 complex, subunit H / ATP synthase complex subunit h / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / 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 / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / 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, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / Peroxidase; domain 1 / 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. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit d, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit H, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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
Revision 2.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / cell / em_software / entity / entity_src_nat / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _cell.Z_PDB / _em_software.category ..._cell.Z_PDB / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _em_software.name / _em_software.version / _entity.pdbx_ec / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
Y: ATP synthase subunit 5, mitochondrial
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
Z: ATP synthase subunit 4, mitochondrial
7: ATP synthase subunit d, mitochondrial
6: ATP synthase subunit H, mitochondrial
U: ATP synthase subunit f, mitochondrial
8: ATP synthase protein 8
X: ATP synthase subunit a
J: ATP synthase subunit J, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,36432
Polymers570,98827
Non-polymers2,3765
Water00
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 ... , 13 types, 26 molecules KLMNOPQRSTYABCDEFGHIZ76UXJ

#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 (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P61829
#2: Protein ATP synthase subunit 5, mitochondrial / ATP synthase chain 5 / Oligomycin sensitivity conferral protein / OSCP


Mass: 20901.139 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: P09457
#3: Protein ATP synthase subunit alpha, mitochondrial


Mass: 55007.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07251
#4: Protein ATP synthase subunit beta, mitochondrial


Mass: 51181.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P00830, H+-transporting two-sector ATPase
#5: Protein ATP synthase subunit gamma, mitochondrial / F-ATPase gamma subunit


Mass: 30657.160 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: P38077
#6: Protein ATP synthase subunit delta, mitochondrial / F-ATPase delta subunit


Mass: 14565.385 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: Q12165
#7: Protein ATP synthase subunit epsilon, mitochondrial / ATPase subunit epsilon


Mass: 6618.359 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: P21306
#8: 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
#9: 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
#10: Protein ATP synthase subunit H, mitochondrial


Mass: 10417.298 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: Q12349
#11: 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
#13: 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
#14: 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 , 1 types, 1 molecules 8

#12: 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

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Non-polymers , 2 types, 5 molecules

#15: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#16: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationY

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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 (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
Type: COMPLEX / Entity ID: #1-#14 / 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 FIELD / 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
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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 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_d0.00939444
ELECTRON MICROSCOPYf_angle_d1.11953443
ELECTRON MICROSCOPYf_dihedral_angle_d5.68223776
ELECTRON MICROSCOPYf_chiral_restr0.0616331
ELECTRON MICROSCOPYf_plane_restr0.0086828

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