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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P32563 New Search
32PDB entries
32Biological assembly
32chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2NVJ NMR structures of transmembrane segment from subunit a from the yeast proton V-ATPase Deposited 2006-11-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric（17） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric（31） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric（31） Consistent with protein count
Chain Q 1–840（840 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16 Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric（31） Consistent with protein count
Chain Q 1–840（840 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7TAO Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase Deposited 2021-12-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric（31） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric（31） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric（31） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric（19） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric（23） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric（16） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric（32） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric（32） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.