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- PDB-6za9: Fo domain of Ovine ATP synthase -

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Basic information

Entry
Database: PDB / ID: 6za9
TitleFo domain of Ovine ATP synthase
Components(ATP synthase ...) x 10
KeywordsMEMBRANE PROTEIN / ATP synthase / mitochondrial / respiratory chain / mammalian
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / 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 motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / lipid binding
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / 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
CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-S12 / ATP synthase protein 8 / ATP synthase 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 ...CARDIOLIPIN / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-S12 / ATP synthase protein 8 / ATP synthase 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsPinke, G. / Zhou, L. / Sazanov, L.A.
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Dec 30, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_mon_prot_cis / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_software.category / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
1: ATP synthase F(0) complex subunit C1, mitochondrial
2: ATP synthase F(0) complex subunit C1, mitochondrial
3: ATP synthase F(0) complex subunit C1, mitochondrial
4: ATP synthase F(0) complex subunit C1, mitochondrial
5: ATP synthase F(0) complex subunit C1, mitochondrial
6: ATP synthase F(0) complex subunit C1, mitochondrial
7: ATP synthase F(0) complex subunit C1, mitochondrial
8: ATP synthase F(0) complex subunit C1, mitochondrial
K: ATP synthase subunit b
M: ATP synthase subunit d, mitochondrial
N: ATP synthase subunit a
O: ATP synthase membrane subunit DAPIT
P: ATP synthase membrane subunit 6.8PL
Q: ATP synthase protein 8
R: ATP synthase membrane subunit f
S: ATP synthase subunit
T: ATP synthase subunit e, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,55927
Polymers237,30517
Non-polymers9,25410
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area69670 Å2
ΔGint-658 kcal/mol
Surface area54540 Å2
MethodPISA

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Components

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ATP synthase ... , 10 types, 17 molecules 12345678KMNOPQRST

#1: Protein
ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase proteolipid P1 / ATPase protein 9 / ATPase subunit c


Mass: 14201.577 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P17605
#2: Protein ATP synthase subunit b /


Mass: 28844.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_004002367.2 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QEA9
#3: Protein ATP synthase subunit d, mitochondrial /


Mass: 18747.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PP37
#4: Protein ATP synthase subunit a / / F-ATPase protein 6


Mass: 24811.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78752
#5: Protein ATP synthase membrane subunit DAPIT


Mass: 6443.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATP synthase membrane subunit DAPIT / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P5H1
#6: Protein ATP synthase membrane subunit 6.8PL


Mass: 6846.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P913
#7: Protein ATP synthase protein 8 / / A6L / F-ATPase subunit 8


Mass: 7918.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78751
#8: Protein ATP synthase membrane subunit f / ATP synthase subunit f / mitochondrial


Mass: 10315.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATP synthase subunit f, XP_004016938.3 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QB48
#9: Protein ATP synthase subunit /


Mass: 11428.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_011950914.1, ATP synthase subunit g / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q5U7
#10: Protein ATP synthase subunit e, mitochondrial /


Mass: 8336.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: XP_027827162.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PF18

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Non-polymers , 3 types, 10 molecules

#11: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#12: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#13: Chemical ChemComp-S12 / O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine / 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine


Type: L-peptide linking / Mass: 523.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46NO9P

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Details

Has ligand of interestN

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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: Fo domain of purified ATP synthase from sheep heart mitochondria
Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 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
SpecimenConc.: 2.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 131951 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 106 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3053 / Details: 40 frames per movie
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
2Gautomatch0.56particle selection
3EPUimage acquisition
5CTFFIND4.1.13CTF correction
8Coot0.8.9model fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14PHENIX1.12_2829model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 809000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217266 / Symmetry type: POINT
Atomic model buildingB value: 77 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 5ARA

5ara


Accession code: 5ARA / Source name: PDB / Type: experimental model

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