Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25

V-type proton ATPase subunit d

OrganismNot specified

UniProt P32366

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain B； UniProt 1–345	Not recorded	;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain Q 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain Q 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain Q 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 8.30 Å
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain P 4–155（152 aa） Chain P 176–201（26 aa） Chain P 284–341（58 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane	Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain Q 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain Q 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain Q 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 1–345（345 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain d 1–345（345 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain d 1–345（345 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–345（345 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–345（345 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–345（345 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain D 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain S 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain S 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain S 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 1–345（345 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 1–345（345 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–345（345 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–345（345 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–345（345 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain d 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain d 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain d 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain B 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain B 1–345（345 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain S 1–345（345 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain S 1–345（345 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

32 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VA0D_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–345； UniProt 1–345

;V-type proton ATPase subunit c'' ;

OrganismNot specified

UniProt P23968

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain C； UniProt 1–213	Not recorded	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain B 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane	Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain R 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain R 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain R 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 16–213（198 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 16–213（198 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain c 1–213（213 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain c 1–213（213 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain c 1–213（213 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain c 1–213（213 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain c 1–213（213 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain G 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain G 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain T 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain T 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain T 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 1–213（213 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 1–213（213 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain c 1–213（213 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain c 1–213（213 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain c 1–213（213 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain c 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain c 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain c 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain C 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain C 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain T 1–213（213 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain T 1–213（213 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATO_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–213； UniProt 1–213

;V-type proton ATPase subunit c' ;

OrganismNot specified

UniProt P32842

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain D； UniProt 1–164	Not recorded	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain D 17–163（147 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane	Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain S 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain S 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain S 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain D 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain D 7–164（158 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain D 7–164（158 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain o 1–164（164 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain o 1–164（164 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain o 1–164（164 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain o 1–164（164 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain o 1–164（164 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain H 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain H 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain U 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain U 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain U 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain D 1–164（164 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain D 1–164（164 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain o 1–164（164 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain o 1–164（164 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain o 1–164（164 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain o 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain o 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain o 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain D 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain D 1–164（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain U 1–164（164 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain U 1–164（164 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATL2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–164； UniProt 1–164

V-type proton ATPase subunit c

OrganismNot specified

UniProt P25515

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain E； UniProt 1–160 Chain F； UniProt 1–160 Chain G； UniProt 1–160 Chain H； UniProt 1–160 Chain I； UniProt 1–160 Chain J； UniProt 1–160 Chain K； UniProt 1–160 Chain L； UniProt 1–160	Not recorded	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain R 1–160（160 aa） Chain S 1–160（160 aa） Chain T 1–160（160 aa） Chain U 1–160（160 aa） Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain R 1–160（160 aa） Chain S 1–160（160 aa） Chain T 1–160（160 aa） Chain U 1–160（160 aa） Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain R 1–160（160 aa） Chain S 1–160（160 aa） Chain T 1–160（160 aa） Chain U 1–160（160 aa） Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 8.30 Å
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain E 9–158（150 aa） Chain F 9–158（150 aa） Chain G 9–158（150 aa） Chain H 9–158（150 aa） Chain I 9–158（150 aa） Chain J 9–158（150 aa） Chain M 9–158（150 aa） Chain N 9–158（150 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane	Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain T 1–160（160 aa） Chain U 1–160（160 aa） Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain T 1–160（160 aa） Chain U 1–160（160 aa） Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain T 1–160（160 aa） Chain U 1–160（160 aa） Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain E 1–160（160 aa） Chain F 1–160（160 aa） Chain G 1–160（160 aa） Chain H 1–160（160 aa） Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain E 1–159（159 aa） Chain F 1–159（159 aa） Chain G 1–159（159 aa） Chain H 1–159（159 aa） Chain I 1–159（159 aa） Chain J 1–159（159 aa） Chain K 1–159（159 aa） Chain L 1–159（159 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa） Chain M 1–160（160 aa） Chain N 1–160（160 aa） Chain O 1–160（160 aa） Chain P 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa） Chain M 1–160（160 aa） Chain N 1–160（160 aa） Chain O 1–160（160 aa） Chain P 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa） Chain b 1–160（160 aa） Chain c 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa） Chain b 1–160（160 aa） Chain c 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa） Chain b 1–160（160 aa） Chain c 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain E 1–160（160 aa） Chain F 1–160（160 aa） Chain G 1–160（160 aa） Chain H 1–160（160 aa） Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain E 1–160（160 aa） Chain F 1–160（160 aa） Chain G 1–160（160 aa） Chain H 1–160（160 aa） Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain g 1–160（160 aa） Chain h 1–160（160 aa） Chain i 1–160（160 aa） Chain j 1–160（160 aa） Chain k 1–160（160 aa） Chain l 1–160（160 aa） Chain m 1–160（160 aa） Chain n 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain E 1–160（160 aa） Chain F 1–160（160 aa） Chain G 1–160（160 aa） Chain H 1–160（160 aa） Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain E 1–160（160 aa） Chain F 1–160（160 aa） Chain G 1–160（160 aa） Chain H 1–160（160 aa） Chain I 1–160（160 aa） Chain J 1–160（160 aa） Chain K 1–160（160 aa） Chain L 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa） Chain b 1–160（160 aa） Chain c 1–160（160 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain V 1–160（160 aa） Chain W 1–160（160 aa） Chain X 1–160（160 aa） Chain Y 1–160（160 aa） Chain Z 1–160（160 aa） Chain a 1–160（160 aa） Chain b 1–160（160 aa） Chain c 1–160（160 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

32 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATL1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–160； UniProt 1–160 Author chain F； PDBConstruct 1–160； UniProt 1–160 Author chain G； PDBConstruct 1–160； UniProt 1–160 Author chain H； PDBConstruct 1–160； UniProt 1–160 Author chain I； PDBConstruct 1–160； UniProt 1–160 Author chain J； PDBConstruct 1–160； UniProt 1–160 Author chain K； PDBConstruct 1–160； UniProt 1–160 Author chain L； PDBConstruct 1–160； UniProt 1–160

V-type proton ATPase subunit e

OrganismNot specified

UniProt Q3E7B6

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain M； UniProt 1–73	Not recorded	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain L 5–61（57 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane	Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain c 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain c 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain c 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–71（71 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–71（71 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain e 1–73（73 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain e 1–73（73 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–73（73 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–73（73 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–73（73 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain E 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain E 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain d 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–73（73 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–73（73 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–73（73 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–73（73 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–73（73 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain e 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain e 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain M 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain M 1–73（73 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain d 1–73（73 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain d 1–73（73 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VA0E_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–73； UniProt 1–73

V0 assembly protein 1

OrganismNot specified

UniProt P53262

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain N； UniProt 1–265	Not recorded	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain N 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain N 212–263（52 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain N 212–263（52 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain b 1–265（265 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain b 1–265（265 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain b 1–265（265 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain b 1–265（265 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain b 1–265（265 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain B 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain e 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain N 1–265（265 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain N 1–265（265 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain b 1–265（265 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain b 1–265（265 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain b 1–265（265 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain b 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain b 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain b 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain N 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain N 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain e 1–265（265 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain e 1–265（265 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VOA1_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain N； PDBConstruct 1–265； UniProt 1–265

Yeast V-ATPase subunit f

OrganismNot specified

UniProt P0C5R9

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain O； UniProt 1–85	Not recorded	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Nanobody 1WVA25 × 4 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain O 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain O 7–75（69 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain O 7–75（69 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain f 1–85（85 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 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain f 1–85（85 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 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 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 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 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
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 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 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain F 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain F 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain O 1–85（85 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain O 1–85（85 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain f 1–85（85 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain f 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain f 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain O 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain O 1–85（85 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain f 1–85（85 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain f 1–85（85 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YP17B_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain O； PDBConstruct 1–85； UniProt 1–85

V-type proton ATPase subunit a, vacuolar isoform

OrganismNot specified

UniProt P32563

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 heterocomplex Heteromer Protein × 19 PDB declaration: 19-meric（19） Consistent with protein copy count	Chain A； UniProt 1–840	Mutation：C-terminal calmodulin binding peptide	V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast V-ATPase subunit f × 1 （P0C5R9） Nanobody 1WVA25 × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE；LEICA EM GP2	Resolution 3.40 Å

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 9E76	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NVJ NMR structures of transmembrane segment from subunit a from the yeast proton V-ATPase Deposited 2006-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 720–744（25 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 303 K；Pressure ambient NMR sample composition 2mM sMTM7 peptide (natural abundance labeling); 100% d6-DMSO | 100% d6-DMSO	Resolution not provided
2RPW Structure of a peptide derived from H+-V-ATPase subunit a Deposited 2008-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 728–748（21 aa） Fragment：TM7, UNP residues 728-748	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Pressure ambient NMR sample composition 1mM KMTM7, 250mM [U-100% 2H] SDS, 10mM sodium phosphate, 0.3mM DSS, 10% D2O, 90% H2O/10% D2O | 90% H2O/10% D2O	Resolution not provided
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain b 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain b 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain b 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).	Resolution 8.30 Å
5I1M Yeast V-ATPase average of densities, a subunit segment Deposited 2016-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain V 383–840（458 aa） Fragment：a subunit (UNP residues 383-840)	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
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 400–829（430 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane	Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain b 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain b 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain b 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–840（840 aa）	Mutation：C-terminal calmodulin binding peptide	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6HH0 Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles Deposited 2018-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 728–748（21 aa） Fragment：transmembrane helix 7	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O | 90% H2O/10% D2O	Resolution not provided
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 3–827（825 aa）	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 3–827（825 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain a 1–840（840 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 3.20 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain A 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain Q 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain Q 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric	Chain Q 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–840（840 aa）	Not recorded	WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–840（840 aa）	Not recorded	KJL Archazolid A × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain a 1–840（840 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain a 1–840（840 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain a 1–840（840 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain a 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain a 1–840（840 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain A 1–840（840 aa）	Mutation：C-terminal calmodulin binding peptide	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain A 1–840（840 aa）	Mutation：C-terminal calmodulin binding peptide	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2	Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain Q 1–840（840 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain Q 1–840（840 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

31 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPH1_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain A； PDBConstruct 1–840； UniProt 1–840

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.