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3j9v

Yeast V-ATPase state 3

Method: ELECTRON MICROSCOPY Dmax: 254.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain b； UniProt 1–840 Not recorded V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V 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 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 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 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 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
5I1M Yeast V-ATPase average of densities, a subunit segment Deposited 2016-02-05 Different construct 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 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 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 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 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 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）
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-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 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different mutation/modification 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 mutation/modification Different oligomeric state Different experimental conditions 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 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 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 1
Chains and sequence ranges Author chain b； PDBConstruct 1–840； UniProt 1–840

V-type proton ATPase subunit C

OrganismNot specified

UniProt P31412

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain O； UniProt 1–392 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1U7L Crystal Structure of subunit C (vma5p) of the yeast V-ATPase Deposited 2004-08-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–392（392 aa）
Not recorded TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 3350, di-sodium tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.75 Å R-free 0.234
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain O 1–392（392 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain O 1–392（392 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
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 158–277（120 aa） Fragment：C subunit head domain, UNP residues 158-277
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 158–277（120 aa） Fragment：C subunit head domain, UNP residues 158-277
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4EFA Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation Deposited 2012-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 158–277（120 aa） Fragment：UNP Residues 158-277
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.1 M lithium sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M glycine , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.82 Å R-free 0.277
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 O 1–392（392 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 O 1–392（392 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 O 1–392（392 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
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 1–392（392 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 1–392（392 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 1–392（392 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
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 O 1–392（392 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 O 1–392（392 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 O 1–392（392 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain O 1–392（392 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 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 O 1–392（392 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 O 1–392（392 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

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATC_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain O； PDBConstruct 1–392； UniProt 1–392

V-type proton ATPase subunit D

OrganismNot specified

UniProt P32610

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain M； UniProt 1–256 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain M 1–256（256 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain M 1–256（256 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
4RND Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase. Deposited 2014-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–256（256 aa）
Chain C 1–256（256 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium citrate tribasic dehydrate, 1.2 M Ammonium citrate monobasic, ph 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.18 Å R-free 0.232
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain g 1–256（256 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain g 1–256（256 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
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 M 1–256（256 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 M 1–256（256 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 M 1–256（256 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
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 M 1–256（256 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 M 1–256（256 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 M 1–256（256 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
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 M 1–256（256 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 M 1–256（256 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 M 1–256（256 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain M 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain M 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 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 M 1–256（256 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
9NN1 Yeast V1-ATPase bound to Rtc5p Deposited 2025-03-04 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 1–256（256 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 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 M 1–256（256 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

19 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATD_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain M； PDBConstruct 1–256； UniProt 1–256

V-type proton ATPase subunit F

OrganismNot specified

UniProt P39111

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain N； UniProt 1–118 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain N 1–118（118 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain N 1–118（118 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
4IX9 Crystal structure of subunit F of V-ATPase from S. cerevisiae Deposited 2013-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–94（94 aa） Fragment：Coupling and Regulatory Subunit F, UNP residues 1-94
Mutation：I69M Non-standard monomer：Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.33 Å R-free 0.212
4IX9 Crystal structure of subunit F of V-ATPase from S. cerevisiae Deposited 2013-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–94（94 aa） Fragment：Coupling and Regulatory Subunit F, UNP residues 1-94
Mutation：I69M Non-standard monomer：Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.33 Å R-free 0.212
4IX9 Crystal structure of subunit F of V-ATPase from S. cerevisiae Deposited 2013-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–94（94 aa） Fragment：Coupling and Regulatory Subunit F, UNP residues 1-94
Mutation：I69M Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.33 Å R-free 0.212
4IX9 Crystal structure of subunit F of V-ATPase from S. cerevisiae Deposited 2013-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–94（94 aa） Fragment：Coupling and Regulatory Subunit F, UNP residues 1-94
Mutation：I69M Non-standard monomer：Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.33 Å R-free 0.212
4RND Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase. Deposited 2014-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–118（118 aa）
Chain D 1–118（118 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium citrate tribasic dehydrate, 1.2 M Ammonium citrate monobasic, ph 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.18 Å R-free 0.232
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain o 1–118（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
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 N 1–118（118 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 N 1–118（118 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 N 1–118（118 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
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 N 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-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 N 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-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 N 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-PROPANE
Resolution 8.70 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 N 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 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 N 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 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 N 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 6.60 Å
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain N 2–118（117 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 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 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；Leica EM GP2
Resolution 3.60 Å
9NN1 Yeast V1-ATPase bound to Rtc5p Deposited 2025-03-04 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 1–118（118 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 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 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
Resolution 3.90 Å

19 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATF_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain N； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase catalytic subunit A

OrganismNot specified

UniProt P17255

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain A； UniProt 2–283 Chain A； UniProt 738–1071 Chain C； UniProt 2–283 Chain C； UniProt 738–1071 Chain E； UniProt 2–283 Chain E； UniProt 738–1071 Fragment：SEE REMARK 999 V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DFA CRYSTAL STRUCTURE OF PI-SCEI IN C2 SPACE GROUP Deposited 1999-11-18 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 284–737（454 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；323 K；20% PEG 3350, 100MM TRIS-HCL, 100MM KCL, 200MM MGCL2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 323.0K
Resolution 2.00 Å R-free 0.280
1GPP Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I Deposited 2001-11-07 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 284–466（183 aa） Fragment：PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE REMARK 999
Chain A 693–736（44 aa） Fragment：PROTEIN SPLICING DOMAIN, RESIDUES 284-466,693-736, SEE REMARK 999
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；30 % PEG4000, 0.1 M SODIUM CITRATE PH 5.6, 0.2 M NH4-ACETATE
Resolution 1.35 Å R-free 0.189
1JVA CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES Deposited 2001-08-29 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 274–747（474 aa） Fragment：RESIDUES 274-747
Mutation：C284S/H362N/N737S/C738S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.240
1JVA CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES Deposited 2001-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 274–747（474 aa） Fragment：RESIDUES 274-747
Mutation：C284S/H362N/N737S/C738S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.240
1LWS Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence Deposited 2002-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 284–737（454 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 200, na hepes, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.310
1LWT Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free) Deposited 2002-06-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 284–737（454 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；PEG 3550, na citrate, ammonium acetate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.287
1UM2 Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment Deposited 2003-09-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 284–737（454 aa）
Chain C 274–283（10 aa）
Chain C 738–747（10 aa）
Mutation：C284S, H362N Mutation：C738S Mutation：C738S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG 6000, BistrisHCl, 2-mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.283
1UM2 Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment Deposited 2003-09-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 284–737（454 aa）
Chain D 274–283（10 aa）
Chain D 738–747（10 aa）
Mutation：C284S, H362N Mutation：C738S Mutation：C738S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG 6000, BistrisHCl, 2-mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.283
1VDE PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY Deposited 1997-04-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 284–737（454 aa）
Chain B 284–737（454 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；4% PEG 6K, 10MM BME, 3MM CDCL2, 1MM MGCL2, 100MM TRIS, PH=8.5
Resolution 2.40 Å R-free 0.238
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain A 2–283（282 aa） Fragment：SEE REMARK 999
Chain A 738–1071（334 aa） Fragment：SEE REMARK 999
Chain C 2–283（282 aa） Fragment：SEE REMARK 999
Chain C 738–1071（334 aa） Fragment：SEE REMARK 999
Chain E 2–283（282 aa） Fragment：SEE REMARK 999
Chain E 738–1071（334 aa） Fragment：SEE REMARK 999
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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain A 2–283（282 aa） Fragment：SEE REMARK 999
Chain A 738–1071（334 aa） Fragment：SEE REMARK 999
Chain C 2–283（282 aa） Fragment：SEE REMARK 999
Chain C 738–1071（334 aa） Fragment：SEE REMARK 999
Chain E 2–283（282 aa） Fragment：SEE REMARK 999
Chain E 738–1071（334 aa） Fragment：SEE REMARK 999
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
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–283（283 aa）
Chain A 738–1071（334 aa）
Chain B 1–283（283 aa）
Chain B 738–1071（334 aa）
Chain C 1–283（283 aa）
Chain C 738–1071（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain a 1–283（283 aa）
Chain a 738–1071（334 aa）
Chain b 1–283（283 aa）
Chain b 738–1071（334 aa）
Chain c 1–283（283 aa）
Chain c 738–1071（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–283（283 aa）
Chain A 738–1071（334 aa）
Chain B 1–283（283 aa）
Chain B 738–1071（334 aa）
Chain C 1–283（283 aa）
Chain C 738–1071（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain a 1–283（283 aa）
Chain a 738–1071（334 aa）
Chain b 1–283（283 aa）
Chain b 738–1071（334 aa）
Chain c 1–283（283 aa）
Chain c 738–1071（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain A 1–283（283 aa）
Chain A 738–1071（334 aa）
Chain C 1–283（283 aa）
Chain C 738–1071（334 aa）
Chain E 1–283（283 aa）
Chain E 738–1071（334 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain A 1–283（283 aa）
Chain A 738–1071（334 aa）
Chain C 1–283（283 aa）
Chain C 738–1071（334 aa）
Chain E 1–283（283 aa）
Chain E 738–1071（334 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain A 1–283（283 aa）
Chain A 738–1071（334 aa）
Chain C 1–283（283 aa）
Chain C 738–1071（334 aa）
Chain E 1–283（283 aa）
Chain E 738–1071（334 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
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain A 1–1071（1071 aa）
Chain E 1–1071（1071 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATA_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain A； PDBConstruct 1–282； UniProt 2–283 Author chain A； PDBConstruct 283–616； UniProt 738–1071 Author chain C； PDBConstruct 1–282； UniProt 2–283 Author chain C； PDBConstruct 283–616； UniProt 738–1071 Author chain E； PDBConstruct 1–282； UniProt 2–283 Author chain E； PDBConstruct 283–616； UniProt 738–1071

V-type proton ATPase subunit B

OrganismNot specified

UniProt P16140

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain B； UniProt 1–517 Chain D； UniProt 1–517 Chain F； UniProt 1–517 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain D 1–517（517 aa）
Chain E 1–517（517 aa）
Chain F 1–517（517 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain d 1–517（517 aa）
Chain e 1–517（517 aa）
Chain f 1–517（517 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 1–517（517 aa）
Chain E 1–517（517 aa）
Chain F 1–517（517 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain d 1–517（517 aa）
Chain e 1–517（517 aa）
Chain f 1–517（517 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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
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 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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
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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain B 1–517（517 aa）
Chain F 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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
9NN1 Yeast V1-ATPase bound to Rtc5p Deposited 2025-03-04 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 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 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 B 1–517（517 aa）
Chain D 1–517（517 aa）
Chain F 1–517（517 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

18 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATB_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain B； PDBConstruct 1–517； UniProt 1–517 Author chain D； PDBConstruct 1–517； UniProt 1–517 Author chain F； PDBConstruct 1–517； UniProt 1–517

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain Q； UniProt 1–345 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V 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 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 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
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
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 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 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 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 7
Chains and sequence ranges Author chain Q； PDBConstruct 1–345； UniProt 1–345

V-type proton ATPase subunit G

OrganismNot specified

UniProt P48836

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain H； UniProt 1–114 Chain J； UniProt 1–114 Chain L； UniProt 1–114 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2K88 Association of subunit d (Vma6p) and E (Vma4p) with G (Vma10p) and the NMR solution structure of subunit G (G1-59) of the Saccharomyces cerevisiae V1VO ATPase Deposited 2008-09-04 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 2–58（57 aa） Fragment：G(1-59)subunit of V1Vo ATPase
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；288 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KWY Structure of G61-101 Deposited 2010-04-22 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 61–101（41 aa） Fragment：UNP residues 61-101
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 200；Pressure AMBIENT
NMR sample composition 7 % D2O-1, 30 % [U-100% 2H] TFE-2, 25 mM sodium phosphate-3, 200 mM sodium chloride-4, Phosphate Buffer pH 6.8 | Phosphate Buffer pH 6.8
Resolution not provided
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–114（114 aa）
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–114（114 aa）
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4EFA Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation Deposited 2012-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–114（114 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.1 M lithium sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M glycine , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.82 Å R-free 0.277
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain J 2–114（113 aa）
Chain L 2–114（113 aa）
Chain N 2–114（113 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain j 2–114（113 aa）
Chain l 2–114（113 aa）
Chain n 2–114（113 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain J 2–114（113 aa）
Chain L 2–114（113 aa）
Chain N 2–114（113 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain j 2–114（113 aa）
Chain l 2–114（113 aa）
Chain n 2–114（113 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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
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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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
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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–114（114 aa）
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 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 H 1–114（114 aa）
Chain J 1–114（114 aa）
Chain L 1–114（114 aa）
Mutation：N-terminal FLAG tag Mutation：N-terminal FLAG tag Mutation：N-terminal FLAG tag ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

20 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATG_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain H； PDBConstruct 1–114； UniProt 1–114 Author chain J； PDBConstruct 1–114； UniProt 1–114 Author chain L； PDBConstruct 1–114； UniProt 1–114

V-type proton ATPase subunit E

OrganismNot specified

UniProt P22203

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain G； UniProt 1–233 Chain I； UniProt 1–233 Chain K； UniProt 1–233 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit H × 1 （P41807） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KZ9 Structure of E1-69 of Yeast V-ATPase Deposited 2010-06-14 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 1–69（69 aa） Fragment：UNP residues 1-69
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 200；Pressure AMBIENT
NMR sample composition 2 mM [U-100% 13C; U-100% 15N] protein-1, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–233（233 aa）
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–233（233 aa）
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4EFA Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation Deposited 2012-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–233（233 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.1 M lithium sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M glycine , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.82 Å R-free 0.277
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Chain M 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain i 1–233（233 aa）
Chain k 1–233（233 aa）
Chain m 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Chain M 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain i 1–233（233 aa）
Chain k 1–233（233 aa）
Chain m 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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
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 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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
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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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
9NN1 Yeast V1-ATPase bound to Rtc5p Deposited 2025-03-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 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 G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 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

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

View Construct and Data Evidence
UniProt name VATE_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain G； PDBConstruct 1–233； UniProt 1–233 Author chain I； PDBConstruct 1–233； UniProt 1–233 Author chain K； PDBConstruct 1–233； UniProt 1–233

V-type proton ATPase subunit H

OrganismNot specified

UniProt P41807

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain P； UniProt 1–478 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit c × 10 （P25515） 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

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 3J9V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HO8 CRYSTAL STRUCTURE OF THE REGULATORY SUBUNIT H OF THE V-TYPE ATPASE OF SACCHAROMYCES CEREVISIAE Deposited 2000-12-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ammonium sulfate, Dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.312
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain P 1–478（478 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain P 1–478（478 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
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain H 1–478（478 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain h 1–478（478 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain H 1–478（478 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain h 1–478（478 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
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 P 1–478（478 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 P 1–478（478 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 P 1–478（478 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
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 P 1–478（478 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 P 1–478（478 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 P 1–478（478 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
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain P 1–359（359 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain P 1–359（359 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain P 1–359（359 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
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 P 1–478（478 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain P 1–478（478 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain P 1–478（478 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain P 1–478（478 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 P 1–478（478 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 P 1–478（478 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 P 1–478（478 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
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain P 1–478（478 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 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 P 1–478（478 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 P 1–478（478 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 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATH_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain P； PDBConstruct 1–478； UniProt 1–478

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 × 28 PDB declaration: 28-meric（28） Consistent with protein copy count Chain R； UniProt 1–160 Chain S； UniProt 1–160 Chain T； UniProt 1–160 Chain U； UniProt 1–160 Chain V； UniProt 1–160 Chain W； UniProt 1–160 Chain X； UniProt 1–160 Chain Y； UniProt 1–160 Chain Z； UniProt 1–160 Chain a； UniProt 1–160 Not recorded V-type proton ATPase subunit a, vacuolar isoform × 1 （P32563） V-type proton ATPase subunit C × 1 （P31412） V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase catalytic subunit A × 3 （P17255） V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit d × 1 （P32366） V-type proton ATPase subunit G × 3 （P48836） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit H × 1 （P41807） 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

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 3J9V 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 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 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
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 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 construct 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 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 construct 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 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 construct 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 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 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 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 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 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 mutation/modification 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 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 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct 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 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 construct Different mutation/modification 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 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 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 construct Different mutation/modification 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
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct 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 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 construct 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 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 11
Chains and sequence ranges Author chain R； PDBConstruct 1–160； UniProt 1–160 Author chain S； PDBConstruct 1–160； UniProt 1–160 Author chain T； PDBConstruct 1–160； UniProt 1–160 Author chain U； PDBConstruct 1–160； UniProt 1–160 Author chain V； PDBConstruct 1–160； UniProt 1–160 Author chain W； PDBConstruct 1–160； UniProt 1–160 Author chain X； PDBConstruct 1–160； UniProt 1–160 Author chain Y； PDBConstruct 1–160； UniProt 1–160 Author chain Z； PDBConstruct 1–160； UniProt 1–160 Author chain a； PDBConstruct 1–160； UniProt 1–160

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 3j9v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j9v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3j9v
Deposition date deposition_date2015-02-23
Structure title titleYeast V-ATPase state 3
Keywords keywordsV-ATPase, V-type ATPase, vacuolar-type ATPase, proton pump, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier74.22 Å
Radius of gyration Rg (electron density) rg_electron75.13 Å
Forward intensity I(0) i08742570000.00
Molecular weight molecular_weight819230.0 kDa
Excluded volume excluded_volume1036300 ų
Envelope volume envelope_volume1560000 ų
Hydration-shell volume shell_volume174620 ų
Envelope diameter envelope_diameter252.4 Å
Shell Rg shell_rg74.71 Å
Envelope Rg envelope_rg72.29 Å
Shape Rg shape_rg75.09 Å
Total Rg total_rg75.28 Å
Total atoms total_atoms57659
Residues n_residues7451
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 dmax254.4 Å
Rg (real space) rg_real74.70 Å
Rg uncertainty (real space) rg_real_error1.95 Å
I(0) (real space) i0_real8.7480e+09
I(0) uncertainty (real space) i0_real_error1.9560e+08
Rg (reciprocal space) rg_reciprocal73.47 Å
I(0) (reciprocal space) i0_reciprocal8726000000.0000
Solution quality estimate total_estimate0.8273
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary72.7 Å
Skewness Skewness skewness0.439
Kurtosis Kurtosis kurtosis-0.363
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0839
Highest regularization parameter α highest_alpha1914000000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.820; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.301
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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8. Citations (1)

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9. Files and Curves (10)