5bqj

Structure of the yeast F1FO ATPase C10 ring with 21-hydroxy-oligomycin

Method: X-RAY DIFFRACTION D_max: 86.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit 9, mitochondrial

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 2–76 Chain B； UniProt 2–76 Chain C； UniProt 2–76 Chain D； UniProt 2–76 Chain E； UniProt 2–76	Non-standard monomer：Yes (specific site not provided by mmCIF)	E21 21-hydroxy-oligomycin × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.10 Å R-free 0.237
2	Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain K； UniProt 2–76 Chain L； UniProt 2–76 Chain M； UniProt 2–76 Chain N； UniProt 2–76 Chain O； UniProt 2–76	Non-standard monomer：Yes (specific site not provided by mmCIF)	E21 21-hydroxy-oligomycin × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.10 Å R-free 0.237

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5BQJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WPD The Mg.ADP inhibited state of the yeast F1c10 ATP synthase Deposited 2009-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M HEPES/HCL PH 7.5, 12% PEG MME 5000, 100 MM SODIUM CHLORIDE MIXED 1:1 WITH PROTEIN SOLUTION CONTAINING 0.64 MM DDM, 25 MM TRIS/HCL PH 8.0, 100 MM SODIUM CHLORIDE, 25 MM TREHALOSE, 0.5 MM EDTA, 0.02% SODIUM AZIDE, 2 MM MAGNESIUM CHLORIDE, 0.66 MM ADP, 0.1 MM DCCD, 2.5 MM DTT, 0.5 MM PMSF	Resolution 3.43 Å R-free 0.297
2XOK Refined structure of yeast F1c10 ATPase complex to 3 A resolution Deposited 2010-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa） Chain T 1–76（76 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；0.1 M TRIS/CL PH8.0, 12% PEG 6000, 150 MM NACL, 1 MM AMP-PNP, 40 MICROM ADP, 1 MM DTT, 0.02% NAN3. MIXED 1:1 WITH PROTEIN SOLUTION UNDER PARAFFIN OIL IN MICROBATCH PLATE.	Resolution 3.01 Å R-free 0.253
3U2F ATP synthase c10 ring in proton-unlocked conformation at PH 8.3 Deposited 2011-10-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；294 K；68% MPD, 8% PROPYLENE GLYCOL, 0.3M NACL, 0.1M MALONATE PH 7.0, 2MM MGSO4, 50MM BICINE, PH 8.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K	Resolution 2.00 Å R-free 0.216
3U2Y ATP synthase c10 ring in proton-unlocked conformation at pH 6.1 Deposited 2011-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；294 K；68% MPD, 8% propolyene glycol, 0.3M NaCl, 0.1M malonate pH 7.0, 2mM MgSO4, 50 mM MES pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.50 Å R-free 0.227
3U32 ATP synthase c10 ring reacted with DCCD at pH 5.5 Deposited 2011-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	DCW DICYCLOHEXYLUREA × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；294 K；68% MPD, 8% propolyene glycol, 0.3M NaCl, 2mM MgSO4, 50 mM MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.00 Å R-free 0.254
3UD0 ATP synthase C10 ring in proton-unlocked conformation at PH 5.5 Deposited 2011-10-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；68% MPD, 8% PROPOLYENE GLYCOL, 0.3M NACL, 0.1M MALONATE PH 7.0, 2MM MGSO4, 50 MM MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K. SOAKING: 68% MPD, 8% PROPYLENE GLYCOL, 0.4M NACL, 2MM MGCL2, 50MM MES PH 5.5, FOR 12 HOURS AT 294K.	Resolution 2.00 Å R-free 0.221
3ZRY Rotor architecture in the F(1)-c(10)-ring complex of the yeast F-ATP synthase Deposited 2011-06-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；10% PEG 4000, 100 MM SODIUM CHLORIDE, 100 MM HEPES PH 6.5 MIXED 1:1 WITH PROTEIN SOLUTION (10 MG/ML) CONTAINING 0.64 MM DDM, 25 MM TRIS PH 8.0, 100 MM SODIUM CHLORIDE, 25 MM TREHALOSE, 0.5 MM EDTA, 3 MM SODIUM AZIDE, 2 MM MAGNESIUM CHLORIDE, 0.04 MM ADP, 1 MM AMP-PNP, 0.1 MM DCCD, 2.5 MM DTT, 0.5 MM PMSF.	Resolution 6.50 Å R-free 0.339
4B2Q Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average Deposited 2012-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric	Chain J 1–76（76 aa） Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa） Chain j 1–76（76 aa） Chain k 1–76（76 aa） Chain l 1–76（76 aa） Chain m 1–76（76 aa） Chain n 1–76（76 aa） Chain o 1–76（76 aa） Chain p 1–76（76 aa） Chain q 1–76（76 aa） Chain r 1–76（76 aa） Chain s 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer 250MM TREHALOSE 10NM TRIS- HCL PH7.4；pH 7.4；250MM TREHALOSE 10NM TRIS- HCL PH7.4 cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 100, INSTRUMENT- HOMEMADE PLUNGER, METHOD- SINGLE SIDE MANUAL BLOTTING FOR 5 SECONDS.,	Resolution 37.00 Å
4F4S Structure of the yeast F1Fo ATPase c10 ring with bound oligomycin Deposited 2012-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa） Chain D 1–76（76 aa） Chain E 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFO Oligomycin A × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；68% MPD, 8% PROPYLENE GLYCOL, 0.3M NACL, 2MM MGSO4, 50MM MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.228
4F4S Structure of the yeast F1Fo ATPase c10 ring with bound oligomycin Deposited 2012-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFO Oligomycin A × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；68% MPD, 8% PROPYLENE GLYCOL, 0.3M NACL, 2MM MGSO4, 50MM MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.228
5BPS Structure of the yeast F1FO ATPase C10 ring with oligomycin A Deposited 2015-05-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 2–76（75 aa） Chain B 2–76（75 aa） Chain C 2–76（75 aa） Chain D 2–76（75 aa） Chain E 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFO Oligomycin A × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.10 Å R-free 0.239
5BPS Structure of the yeast F1FO ATPase C10 ring with oligomycin A Deposited 2015-05-28	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 2–76（75 aa） Chain L 2–76（75 aa） Chain M 2–76（75 aa） Chain N 2–76（75 aa） Chain O 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFO Oligomycin A × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.10 Å R-free 0.239
5BQ6 Structure of the yeast F1FO ATPase C10 ring with oligomycin B Deposited 2015-05-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 2–76（75 aa） Chain B 2–76（75 aa） Chain C 2–76（75 aa） Chain D 2–76（75 aa） Chain E 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFB oligomycin B × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.30 Å R-free 0.247
5BQ6 Structure of the yeast F1FO ATPase C10 ring with oligomycin B Deposited 2015-05-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 2–76（75 aa） Chain L 2–76（75 aa） Chain M 2–76（75 aa） Chain N 2–76（75 aa） Chain O 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFB oligomycin B × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.30 Å R-free 0.247
5BQA Structure of the yeast F1FO ATPase C10 ring with oligomycin C Deposited 2015-05-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 2–76（75 aa） Chain B 2–76（75 aa） Chain C 2–76（75 aa） Chain D 2–76（75 aa） Chain E 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EF4 oligomycin C × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.10 Å R-free 0.250
5BQA Structure of the yeast F1FO ATPase C10 ring with oligomycin C Deposited 2015-05-28	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 2–76（75 aa） Chain L 2–76（75 aa） Chain M 2–76（75 aa） Chain N 2–76（75 aa） Chain O 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EF4 oligomycin C × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；68% MPD, 8% propylene glycol, 0.3 M sodium chloride, 2 mM magnesium sulfate, 50 mM MES, pH 5.5	Resolution 2.10 Å R-free 0.250
6B2Z Cryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase Deposited 2017-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 38 PDB declaration: 38-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa） Chain D 1–76（76 aa） Chain E 1–76（76 aa） Chain F 1–76（76 aa） Chain G 1–76（76 aa） Chain H 1–76（76 aa） Chain I 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；blot for 26 seconds before plunging	Resolution 3.60 Å
6B8H Mosaic model of yeast mitochondrial ATP synthase monomer Deposited 2017-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa） Chain J 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa） Chain T 1–76（76 aa） Chain U 1–76（76 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 10 MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.60 Å
6CP3 Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound. Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa） Chain T 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-HCl, 150 mM NaCl, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6CP5 Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement. Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain K 2–76（75 aa） Chain L 2–76（75 aa） Chain M 2–76（75 aa） Chain N 2–76（75 aa） Chain O 2–76（75 aa） Chain P 2–76（75 aa） Chain Q 2–76（75 aa） Chain R 2–76（75 aa） Chain S 2–76（75 aa） Chain T 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EFO Oligomycin A × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-HCl, 150 mM NaCl, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6CP6 Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc. Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa） Chain T 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-HCl, 150 mM NaCl, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6CP7 Monomer yeast ATP synthase Fo reconstituted in nanodisc generated from masked refinement. Deposited 2018-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain K 1–76（76 aa） Chain L 1–76（76 aa） Chain M 1–76（76 aa） Chain N 1–76（76 aa） Chain O 1–76（76 aa） Chain P 1–76（76 aa） Chain Q 1–76（76 aa） Chain R 1–76（76 aa） Chain S 1–76（76 aa） Chain T 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-HCl, 150 mM NaCl, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6WTD Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of Bedaquiline bound Deposited 2020-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain K 2–76（75 aa） Chain L 2–76（75 aa） Chain M 2–76（75 aa） Chain N 2–76（75 aa） Chain O 2–76（75 aa） Chain P 2–76（75 aa） Chain Q 2–76（75 aa） Chain R 2–76（75 aa） Chain S 2–76（75 aa） Chain T 2–76（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-HCl, 150 mM NaCl, pH 8.0 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7TK2 Yeast ATP synthase State 1binding(a) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.50 Å
7TK3 Yeast ATP synthase State 1binding(b) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.30 Å
7TK4 Yeast ATP synthase State 1binding(c) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å
7TK5 Yeast ATP synthase State 1binding(d) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.80 Å
7TK6 Yeast ATP synthase State 1catalytic(a) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.50 Å
7TK7 Yeast ATP synthase State 1catalytic(b) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.70 Å
7TK8 Yeast ATP synthase State 1catalytic(c) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.70 Å
7TK9 Yeast ATP synthase State 1catalytic(d) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.00 Å
7TKA Yeast ATP synthase State 1catalytic(e) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.10 Å
7TKB Yeast ATP synthase State 1catalytic(f) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.30 Å
7TKC Yeast ATP synthase State 1catalytic(g) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.80 Å
7TKD Yeast ATP synthase State 1catalytic(h) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
7TKE Yeast ATP synthase State 2binding(a) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.10 Å
7TKF Yeast ATP synthase State 2binding(b) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.10 Å
7TKG Yeast ATP synthase State 2catalytic(a) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
7TKH Yeast ATP synthase State 2catalytic(b) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
7TKI Yeast ATP synthase State 2catalytic(c) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.10 Å
7TKJ Yeast ATP synthase State 2catalytic(d) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.50 Å
7TKK Yeast ATP synthase State 2catalytic(e) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.30 Å
7TKL Yeast ATP synthase State 3binding(a) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.40 Å
7TKM Yeast ATP synthase State 3binding(b) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
7TKN Yeast ATP synthase State 3binding(c) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.10 Å
7TKO Yeast ATP synthase State 3catalytic(a) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.80 Å
7TKP Yeast ATP synthase State 3catalytic(b) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.60 Å
7TKQ Yeast ATP synthase State 3catalytic(c) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
7TKR Yeast ATP synthase State 3catalytic(d) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.50 Å
7TKS Yeast ATP synthase State 3catalytic(e) with 10 mM ATP backbone model Deposited 2022-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain 0 1–76（76 aa） Chain 1 1–76（76 aa） Chain 2 1–76（76 aa） Chain 3 1–76（76 aa） Chain 4 1–76（76 aa） Chain 5 1–76（76 aa） Chain 6 1–76（76 aa） Chain 7 1–76（76 aa） Chain 8 1–76（76 aa） Chain 9 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.50 Å
8F29 Yeast ATP synthase in conformation-1 at pH 6 Deposited 2022-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain K 1–75（75 aa） Chain L 1–75（75 aa） Chain M 1–75（75 aa） Chain N 1–75（75 aa） Chain O 1–75（75 aa） Chain P 1–75（75 aa） Chain Q 1–75（75 aa） Chain R 1–75（75 aa） Chain S 1–75（75 aa） Chain T 1–75（75 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 PO4 PHOSPHATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8F39 Yeast ATP synthase in conformation-2, at pH 6 Deposited 2022-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain K 1–75（75 aa） Chain L 1–75（75 aa） Chain M 1–75（75 aa） Chain N 1–75（75 aa） Chain O 1–75（75 aa） Chain P 1–75（75 aa） Chain Q 1–75（75 aa） Chain R 1–75（75 aa） Chain S 1–75（75 aa） Chain T 1–75（75 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

48 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATP9_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–76； UniProt 2–76 Author chain B； PDBConstruct 2–76； UniProt 2–76 Author chain C； PDBConstruct 2–76； UniProt 2–76 Author chain D； PDBConstruct 2–76； UniProt 2–76 Author chain E； PDBConstruct 2–76； UniProt 2–76 Author chain K； PDBConstruct 2–76； UniProt 2–76 Author chain L； PDBConstruct 2–76； UniProt 2–76 Author chain M； PDBConstruct 2–76； UniProt 2–76 Author chain N； PDBConstruct 2–76； UniProt 2–76 Author chain O； PDBConstruct 2–76； UniProt 2–76

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5bqj
Deposition date deposition_date	2015-05-29
Structure title title	Structure of the yeast F1FO ATPase C10 ring with 21-hydroxy-oligomycin
Keywords keywords	;C10 ring, F1FO ATP synthase, 21-hydroxy-oligomycin, mitochondria, membrane, protein-antibiotic complex, MEMBRANE PROTEIN-ANTIBIOTIC complex ;; MEMBRANE PROTEIN/ANTIBIOTIC
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.44 Å
Radius of gyration Rg (electron density) rg_electron	27.32 Å
Forward intensity I(0) i0	73045300.00
Molecular weight molecular_weight	80905.0 kDa
Excluded volume excluded_volume	107320 Å³
Envelope volume envelope_volume	121980 Å³
Hydration-shell volume shell_volume	36272 Å³
Envelope diameter envelope_diameter	92.7 Å
Shell Rg shell_rg	35.47 Å
Envelope Rg envelope_rg	27.37 Å
Shape Rg shape_rg	27.32 Å
Total Rg total_rg	28.28 Å
Total atoms total_atoms	5698
Residues n_residues	737
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.8 Å
Rg (real space) rg_real	28.23 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	7.3050e+07
I(0) uncertainty (real space) i0_real_error	1.1320e+06
Rg (reciprocal space) rg_reciprocal	28.30 Å
I(0) (reciprocal space) i0_reciprocal	73050000.0000
Solution quality estimate total_estimate	0.8262
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.438
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4101000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	5bqjA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjN00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

Domain ID domain_id	5bqjO00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

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8. Citations (2)

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Unit-cell length a length_a	75.975 Å
Unit-cell length b length_b	75.975 Å
Unit-cell length c length_c	489.218 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	160

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2006
R_work r_work	0.1986
R_free r_free	0.2372

Description description	ATP synthase subunit 9, mitochondrial
Molecular weight formula_weight	7790.4 kDa
EC 编号 ec_number	3.6.-.-
Source method src_method	nat
Copy count entity_count	10

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,K,L,M,N,O
Atom count atom_count	6007

Structure of the yeast F1FO ATPase C10 ring with 21-hydroxy-oligomycin

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit 9, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	21-hydroxy-oligomycin
Molecular weight formula_weight	807.1 kDa
Source method src_method	syn
Copy count entity_count	7

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

fit	/app/data/saxs_computation/bq/5bqj/5bqj.fit
pddf	/app/data/pr_computation/bq/5bqj/5bqj.pr.out
profile	/app/data/saxs_computation/bq/5bqj/5bqj.dat