← Back to search
7fdc

CryoEM Structures of Reconstituted V-ATPase, state3

Method: ELECTRON MICROSCOPY Dmax: 217.5 Å Quality: REASONABLE
▼

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

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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain B； UniProt 1–517 Chain D； UniProt 1–517 Chain F； UniProt 1–517 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 oligomeric state Different experimental conditions 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
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 8.30 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 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 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 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state 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 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 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 2
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 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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain G； UniProt 1–233 Chain I； UniProt 1–233 Chain K； UniProt 1–233 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC 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 oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 8.30 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 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 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 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state 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 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 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 3
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 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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain M； UniProt 1–256 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 oligomeric state Different experimental conditions 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
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 8.30 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 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 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 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state 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 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 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 5
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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain N； UniProt 1–118 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 oligomeric state Different experimental conditions 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
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 8.30 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 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 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 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state 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 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 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 6
Chains and sequence ranges Author chain N； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase subunit C

Saccharomyces cerevisiae S288C

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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain O； UniProt 1–392 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC 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 oligomeric state Different experimental conditions 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 oligomeric state Different experimental conditions 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
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain 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 8.30 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 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 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 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
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different oligomeric state 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 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 7
Chains and sequence ranges Author chain O； PDBConstruct 1–392； UniProt 1–392

Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)

Homo sapiens

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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain P； UniProt 1–359 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC 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 construct 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 construct Different oligomeric state Different experimental conditions 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 construct Different oligomeric state Different experimental conditions 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
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different construct Different oligomeric state Different experimental conditions 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 8.30 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 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 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 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 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 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 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 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different experimental conditions 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 construct 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 construct 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 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 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
7TMM Complete V1 Complex from Saccharomyces cerevisiae Deposited 2022-01-19 Different construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion 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 construct 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 construct Different oligomeric state Different ligand/ion 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 8
Chains and sequence ranges Author chain P； PDBConstruct 1–359； UniProt 1–359

Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)

Homo sapiens

UniProt Q9UI12

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain P； UniProt 356–465 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain P 1–483（483 aa）
Not recorded CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain P 1–483（483 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain P 1–483（483 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain P 356–465（110 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 structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain P 356–465（110 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain P 1–483（483 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain H 1–483（483 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATH_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain P； PDBConstruct 360–469； UniProt 356–465

Yeast Vacuolar ATPase a subunit

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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain Q； UniProt 1–840 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain b 1–840（840 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain b 1–840（840 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain b 1–840（840 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 8.30 Å
5I1M Yeast V-ATPase average of densities, a subunit segment Deposited 2016-02-05 Different construct Different 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 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 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 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 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 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 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 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
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion 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 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 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 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 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain Q 1–840（840 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VPH1_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain Q； PDBConstruct 1–840； UniProt 1–840

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 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain S； UniProt 1–345 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain Q 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain Q 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain Q 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 8.30 Å
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain P 4–155（152 aa）
Chain P 176–201（26 aa）
Chain P 284–341（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane
Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Q 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Q 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain Q 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain B 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain B 1–345（345 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different oligomeric state 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 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 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 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 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 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
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain B 1–345（345 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain B 1–345（345 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain d 1–345（345 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain d 1–345（345 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain d 1–345（345 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain d 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state 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 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain B 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain B 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain S 1–345（345 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain S 1–345（345 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VA0D_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain S； PDBConstruct 1–345； UniProt 1–345

;V-type proton ATPase subunit c'' ;

OrganismNot specified

UniProt P23968

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain T； UniProt 1–213 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain B 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane
Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain R 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain R 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain R 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 16–213（198 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 16–213（198 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain G 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain T 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain T 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 1–213（213 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 1–213（213 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain c 1–213（213 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain c 1–213（213 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain c 1–213（213 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain c 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric
Chain C 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain C 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain C 1–213（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain T 1–213（213 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain T 1–213（213 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VATO_YEAST
Isoform —
PDB entities 11
Chains and sequence ranges Author chain T； PDBConstruct 1–213； UniProt 1–213

;V-type proton ATPase subunit c' ;

OrganismNot specified

UniProt P32842

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain U； UniProt 1–164 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain D 17–163（147 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane
Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain S 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain S 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain S 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 7–164（158 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 7–164（158 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain H 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain U 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain U 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 1–164（164 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 1–164（164 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain o 1–164（164 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain o 1–164（164 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain o 1–164（164 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain o 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric
Chain D 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain D 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain D 1–164（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain U 1–164（164 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain U 1–164（164 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VATL2_YEAST
Isoform —
PDB entities 12
Chains and sequence ranges Author chain U； PDBConstruct 1–164； UniProt 1–164

V-type proton ATPase subunit c

OrganismNot specified

UniProt P25515

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count 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 Chain b； UniProt 1–160 Chain c； UniProt 1–160 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain R 1–160（160 aa）
Chain S 1–160（160 aa）
Chain T 1–160（160 aa）
Chain U 1–160（160 aa）
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain R 1–160（160 aa）
Chain S 1–160（160 aa）
Chain T 1–160（160 aa）
Chain U 1–160（160 aa）
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain R 1–160（160 aa）
Chain S 1–160（160 aa）
Chain T 1–160（160 aa）
Chain U 1–160（160 aa）
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 8.30 Å
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain E 9–158（150 aa）
Chain F 9–158（150 aa）
Chain G 9–158（150 aa）
Chain H 9–158（150 aa）
Chain I 9–158（150 aa）
Chain J 9–158（150 aa）
Chain M 9–158（150 aa）
Chain N 9–158（150 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane
Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain T 1–160（160 aa）
Chain U 1–160（160 aa）
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain T 1–160（160 aa）
Chain U 1–160（160 aa）
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain T 1–160（160 aa）
Chain U 1–160（160 aa）
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain E 1–160（160 aa）
Chain F 1–160（160 aa）
Chain G 1–160（160 aa）
Chain H 1–160（160 aa）
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain E 1–159（159 aa）
Chain F 1–159（159 aa）
Chain G 1–159（159 aa）
Chain H 1–159（159 aa）
Chain I 1–159（159 aa）
Chain J 1–159（159 aa）
Chain K 1–159（159 aa）
Chain L 1–159（159 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain E 1–159（159 aa）
Chain F 1–159（159 aa）
Chain G 1–159（159 aa）
Chain H 1–159（159 aa）
Chain I 1–159（159 aa）
Chain J 1–159（159 aa）
Chain K 1–159（159 aa）
Chain L 1–159（159 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Chain M 1–160（160 aa）
Chain N 1–160（160 aa）
Chain O 1–160（160 aa）
Chain P 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20 Different oligomeric state Different 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 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 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
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain E 1–160（160 aa）
Chain F 1–160（160 aa）
Chain G 1–160（160 aa）
Chain H 1–160（160 aa）
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain E 1–160（160 aa）
Chain F 1–160（160 aa）
Chain G 1–160（160 aa）
Chain H 1–160（160 aa）
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain g 1–160（160 aa）
Chain h 1–160（160 aa）
Chain i 1–160（160 aa）
Chain j 1–160（160 aa）
Chain k 1–160（160 aa）
Chain l 1–160（160 aa）
Chain m 1–160（160 aa）
Chain n 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state Different 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric
Chain E 1–160（160 aa）
Chain F 1–160（160 aa）
Chain G 1–160（160 aa）
Chain H 1–160（160 aa）
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain E 1–160（160 aa）
Chain F 1–160（160 aa）
Chain G 1–160（160 aa）
Chain H 1–160（160 aa）
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain E 1–160（160 aa）
Chain F 1–160（160 aa）
Chain G 1–160（160 aa）
Chain H 1–160（160 aa）
Chain I 1–160（160 aa）
Chain J 1–160（160 aa）
Chain K 1–160（160 aa）
Chain L 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Chain b 1–160（160 aa）
Chain c 1–160（160 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain V 1–160（160 aa）
Chain W 1–160（160 aa）
Chain X 1–160（160 aa）
Chain Y 1–160（160 aa）
Chain Z 1–160（160 aa）
Chain a 1–160（160 aa）
Chain b 1–160（160 aa）
Chain c 1–160（160 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VATL1_YEAST
Isoform —
PDB entities 13
Chains and sequence ranges 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 Author chain b； PDBConstruct 1–160； UniProt 1–160 Author chain c； PDBConstruct 1–160； UniProt 1–160

V-type proton ATPase subunit e

OrganismNot specified

UniProt Q3E7B6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain d； UniProt 1–73 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V0 assembly protein 1 × 1 （P53262） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5TJ5 Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase Deposited 2016-10-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain L 5–61（57 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Modified for ethane/propane
Resolution 3.90 Å
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain c 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain c 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain c 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 1–71（71 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 1–71（71 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain E 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain E 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain d 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain d 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 1–73（73 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain M 1–73（73 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–73（73 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–73（73 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–73（73 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain e 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
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 M 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain M 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain M 1–73（73 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain d 1–73（73 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain d 1–73（73 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VA0E_YEAST
Isoform —
PDB entities 14
Chains and sequence ranges Author chain d； PDBConstruct 1–73； UniProt 1–73

V0 assembly protein 1

OrganismNot specified

UniProt P53262

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain e； UniProt 1–265 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） Yeast Vacuolar ATPase f subunit × 1 （P0C5R9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 212–263（52 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 212–263（52 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain B 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 1–265（265 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain N 1–265（265 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain b 1–265（265 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain b 1–265（265 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain b 1–265（265 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAT Yeast VO missing subunits a, e, and f in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain b 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E76 Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25 Deposited 2024-10-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric
Chain N 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain N 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain N 1–265（265 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain e 1–265（265 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain e 1–265（265 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name VOA1_YEAST
Isoform —
PDB entities 15
Chains and sequence ranges Author chain e； PDBConstruct 1–265； UniProt 1–265

Yeast Vacuolar ATPase f subunit

OrganismNot specified

UniProt P0C5R9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 31 PDB declaration: 31-meric（31） Consistent with protein copy count Chain f； UniProt 1–85 Not recorded Yeast Vacuolar ATPase A subunit × 3 V-type proton ATPase subunit B × 3 （P16140） V-type proton ATPase subunit E × 3 （P22203） V-type proton ATPase subunit G × 3 V-type proton ATPase subunit D × 1 （P32610） V-type proton ATPase subunit F × 1 （P39111） V-type proton ATPase subunit C × 1 （P31412） Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) × 1 （P41807,Q9UI12） Yeast Vacuolar ATPase a subunit × 1 （P32563） V-type proton ATPase subunit d × 1 （P32366） ;V-type proton ATPase subunit c'' ; × 1 （P23968） ;V-type proton ATPase subunit c' ; × 1 （P32842） V-type proton ATPase subunit c × 8 （P25515） V-type proton ATPase subunit e × 1 （Q3E7B6） V0 assembly protein 1 × 1 （P53262） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.60 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 7FDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C6L Yeast Vacuolar ATPase Vo in lipid nanodisc Deposited 2018-01-19 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain O 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6M0R 2.7A Yeast Vo state3 Deposited 2020-02-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain O 7–75（69 aa）
Not recorded PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 30 PPV PYROPHOSPHATE × 1 EYR (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6M0S 3.6A Yeast Vo state3 prime Deposited 2020-02-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain O 7–75（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6O7T Saccharomyces cerevisiae V-ATPase Vph1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
6O7U Saccharomyces cerevisiae V-ATPase Stv1-VO Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
6PE4 Yeast Vo motor in complex with 1 VopQ molecule Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain F 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6PE5 Yeast Vo motor in complex with 2 VopQ molecules Deposited 2019-06-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain O 1–85（85 aa）
Not recorded WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7TAP Cryo-EM structure of archazolid A bound to yeast VO V-ATPase Deposited 2021-12-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain O 1–85（85 aa）
Not recorded KJL Archazolid A × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7TMR V-ATPase from Saccharomyces cerevisiae, State 1 Deposited 2022-01-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7TMS V-ATPase from Saccharomyces cerevisiae, State 2 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7TMT V-ATPase from Saccharomyces cerevisiae, State 3 Deposited 2022-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain f 1–85（85 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
8EAS Yeast VO in complex with Vma12-22p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EAU Yeast VO in complex with Vma21p Deposited 2022-08-29 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain f 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
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 O 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.40 Å
9E7L Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7 Deposited 2024-11-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain O 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9MJ4 Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149 Deposited 2024-12-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain O 1–85（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EM GP2
Resolution 3.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain f 1–85（85 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain f 1–85（85 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name YP17B_YEAST
Isoform —
PDB entities 16
Chains and sequence ranges Author chain f； PDBConstruct 1–85； UniProt 1–85

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 7fdc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7fdc
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7fdc
Deposition date deposition_date2021-07-16
Structure title titleCryoEM Structures of Reconstituted V-ATPase, state3
Keywords keywordsATPase, proton pump, rotary motor enzyme, membrane protein, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier81.21 Å
Radius of gyration Rg (electron density) rg_electron82.17 Å
Forward intensity I(0) i010741200000.00
Molecular weight molecular_weight916190.0 kDa
Excluded volume excluded_volume1161000 ų
Envelope volume envelope_volume1923400 ų
Hydration-shell volume shell_volume196770 ų
Envelope diameter envelope_diameter266.8 Å
Shell Rg shell_rg80.62 Å
Envelope Rg envelope_rg78.30 Å
Shape Rg shape_rg82.14 Å
Total Rg total_rg82.25 Å
Total atoms total_atoms64497
Residues n_residues8295
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
▼

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

Maximum dimension Dmax dmax217.5 Å
Rg (real space) rg_real78.79 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real1.0470e+10
I(0) uncertainty (real space) i0_real_error1.9530e+08
Rg (reciprocal space) rg_reciprocal80.05 Å
I(0) (reciprocal space) i0_reciprocal10710000000.0000
Solution quality estimate total_estimate0.6535
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary80.1 Å
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.652
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha0.1722
Highest regularization parameter α highest_alpha2005000000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 0.984; Sysdev: 0.008; Positv: 1.000; Valcen: 0.995; Smooth: 0.005
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (16)

▶

8. Citations (1)

▶

9. Files and Curves (10)