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8eat

Yeast VO missing subunits a, e, and f in complex with Vma12-22p

Method: ELECTRON MICROSCOPY Dmax: 145.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vacuolar ATPase assembly protein VMA22

OrganismNot specified

UniProt P38784

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain A； UniProt 1–181 Not recorded Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V0 assembly protein 1 × 1 （P53262） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit c × 8 （P25515） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–181（181 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VMA22_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–181； UniProt 1–181

Vacuolar ATPase assembly integral membrane protein VPH2

OrganismNot specified

UniProt P32341

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain B； UniProt 1–215 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V0 assembly protein 1 × 1 （P53262） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit c × 8 （P25515） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name VPH2_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–215； UniProt 1–215

V-type proton ATPase subunit F

OrganismNot specified

UniProt A0A6A5PYF6

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain F； UniProt 1–118 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V0 assembly protein 1 × 1 （P53262） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit c × 8 （P25515） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7TMM Complete V1 Complex from Saccharomyces cerevisiae Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain N 1–118（118 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
7TMO V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 1–118（118 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7TMP V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2 Deposited 2022-01-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 1–118（118 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7TMQ V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3 Deposited 2022-01-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 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 N 1–118（118 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 N 1–118（118 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 N 1–118（118 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 1–118（118 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

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A6A5PYF6_YEASX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain F； PDBConstruct 1–118； UniProt 1–118

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain b； UniProt 1–265 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit c × 8 （P25515） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT 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 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 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 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 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 experimental conditions 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-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 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state 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 experimental conditions 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 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 4
Chains and sequence ranges Author chain b； PDBConstruct 1–265； UniProt 1–265

;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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain c； UniProt 1–213 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V0 assembly protein 1 × 1 （P53262） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit c × 8 （P25515） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT 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 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 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 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 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 experimental conditions 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-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 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state 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 experimental conditions 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 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 5
Chains and sequence ranges Author chain c； PDBConstruct 1–213； UniProt 1–213

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain d； UniProt 1–345 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V0 assembly protein 1 × 1 （P53262） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit c × 8 （P25515） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT 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 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 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 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 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 experimental conditions 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-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 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state 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 experimental conditions 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 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 6
Chains and sequence ranges Author chain d； PDBConstruct 1–345； UniProt 1–345

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count 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 Chain m； UniProt 1–160 Chain n； UniProt 1–160 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V0 assembly protein 1 × 1 （P53262） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c' ; × 1 （P32842） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT 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 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 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 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 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 experimental conditions 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-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 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state 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 experimental conditions 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 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 7
Chains and sequence ranges 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 Author chain m； PDBConstruct 1–160； UniProt 1–160 Author chain n； PDBConstruct 1–160； UniProt 1–160

;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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain o； UniProt 1–164 Not recorded Vacuolar ATPase assembly protein VMA22 × 1 （P38784） Vacuolar ATPase assembly integral membrane protein VPH2 × 1 （P32341） V-type proton ATPase subunit F × 1 （A0A6A5PYF6） V0 assembly protein 1 × 1 （P53262） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit c × 8 （P25515） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EAT 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 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 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 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 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 experimental conditions 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-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 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state 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 experimental conditions 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 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 8
Chains and sequence ranges Author chain o； PDBConstruct 1–164； UniProt 1–164

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

SAXS scattering curve SAXS Profile

SAXS profile for 8eat

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8eat
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8eat
Deposition date deposition_date2022-08-29
Structure title titleYeast VO missing subunits a, e, and f in complex with Vma12-22p
Keywords keywordsV-type proton ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.83 Å
Radius of gyration Rg (electron density) rg_electron42.25 Å
Forward intensity I(0) i0757951000.00
Molecular weight molecular_weight244240.0 kDa
Excluded volume excluded_volume313430 ų
Envelope volume envelope_volume401970 ų
Hydration-shell volume shell_volume79325 ų
Envelope diameter envelope_diameter154.3 Å
Shell Rg shell_rg47.56 Å
Envelope Rg envelope_rg42.04 Å
Shape Rg shape_rg42.28 Å
Total Rg total_rg42.43 Å
Total atoms total_atoms34663
Residues n_residues2349
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax145.6 Å
Rg (real space) rg_real42.92 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real7.5790e+08
I(0) uncertainty (real space) i0_real_error1.1750e+07
Rg (reciprocal space) rg_reciprocal42.83 Å
I(0) (reciprocal space) i0_reciprocal757900000.0000
Solution quality estimate total_estimate0.8079
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.1 Å
Skewness Skewness skewness0.541
Kurtosis Kurtosis kurtosis0.267
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha86870000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.606; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.683
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (2)

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9. Files and Curves (10)