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7unf

CryoEM structure of a mEAK7 bound human V-ATPase complex

Method: ELECTRON MICROSCOPY Dmax: 221.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

V-type proton ATPase 116 kDa subunit a 4

Homo sapiens

UniProt Q9HBG4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain a； UniProt 1–840 Not recorded KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain a 1–840（840 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name VPP4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain a； PDBConstruct 1–840； UniProt 1–840

KIAA1609 protein, isoform CRA_a

OrganismNot specified

UniProt D3DUL8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain U； UniProt 1–456 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UNE The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) Deposited 2022-04-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain U 2–456（455 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å

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

View Construct and Data Evidence
UniProt name D3DUL8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain U； PDBConstruct 1–456； UniProt 1–456

V-type proton ATPase catalytic subunit A

OrganismNot specified

UniProt P38606

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain L； UniProt 1–617 Chain M； UniProt 1–617 Chain N； UniProt 1–617 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å

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

View Construct and Data Evidence
UniProt name VATA_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain L； PDBConstruct 1–617； UniProt 1–617 Author chain M； PDBConstruct 1–617； UniProt 1–617 Author chain N； PDBConstruct 1–617； UniProt 1–617

V-type proton ATPase subunit B, brain isoform

OrganismNot specified

UniProt P21281

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain O； UniProt 1–511 Chain P； UniProt 1–511 Chain Q； UniProt 1–511 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å

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

View Construct and Data Evidence
UniProt name VATB2_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain O； PDBConstruct 1–511； UniProt 1–511 Author chain P； PDBConstruct 1–511； UniProt 1–511 Author chain Q； PDBConstruct 1–511； UniProt 1–511

V-type proton ATPase subunit D

OrganismNot specified

UniProt Q9Y5K8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain D； UniProt 1–247 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain G 1–247（247 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–247（247 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–247（247 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–247（247 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain G 1–247（247 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain G 1–247（247 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain G 1–247（247 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å

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

View Construct and Data Evidence
UniProt name VATD_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain D； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit E 1

OrganismNot specified

UniProt P36543

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain b； UniProt 1–226 Chain c； UniProt 1–226 Chain d； UniProt 1–226 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain H 1–226（226 aa）
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å

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

View Construct and Data Evidence
UniProt name VATE1_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain b； PDBConstruct 1–226； UniProt 1–226 Author chain c； PDBConstruct 1–226； UniProt 1–226 Author chain d； PDBConstruct 1–226； UniProt 1–226

V-type proton ATPase subunit G 1

OrganismNot specified

UniProt O75348

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain e； UniProt 1–118 Chain f； UniProt 1–118 Chain g； UniProt 1–118 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 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 2.90 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 1–118（118 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 1–118（118 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 1–118（118 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 1–118（118 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 1–118（118 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain K 1–118（118 aa）
Chain L 1–118（118 aa）
Chain M 1–118（118 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å

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

View Construct and Data Evidence
UniProt name VATG1_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain e； PDBConstruct 1–118； UniProt 1–118 Author chain f； PDBConstruct 1–118； UniProt 1–118 Author chain g； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase subunit F

OrganismNot specified

UniProt Q16864

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain F； UniProt 1–119 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain N 1–119（119 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain N 1–119（119 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain N 1–119（119 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain N 1–119（119 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain N 1–119（119 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain N 1–119（119 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain N 1–119（119 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å

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

View Construct and Data Evidence
UniProt name VATF_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain F； PDBConstruct 1–119； UniProt 1–119

V-type proton ATPase subunit C 1

OrganismNot specified

UniProt P21283

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain C； UniProt 1–382 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain O 1–382（382 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain O 1–382（382 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain O 1–382（382 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain O 1–382（382 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATC1_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain C； PDBConstruct 1–382； UniProt 1–382

V-type proton ATPase subunit H

OrganismNot specified

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 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain H； UniProt 1–483 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 6.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions 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

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 10
Chains and sequence ranges Author chain H； PDBConstruct 1–483； UniProt 1–483

V-type proton ATPase subunit d 1

OrganismNot specified

UniProt P61421

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain k； UniProt 1–351 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain Q 1–351（351 aa）
Not recorded WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–351（351 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–351（351 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–351（351 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain Q 1–351（351 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain Q 1–351（351 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain Q 1–351（351 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain d 1–351（351 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name VA0D1_HUMAN
Isoform —
PDB entities 11
Chains and sequence ranges Author chain k； PDBConstruct 1–351； UniProt 1–351

V-type proton ATPase subunit e 1

OrganismNot specified

UniProt O15342

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain m； UniProt 1–81 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain S 1–81（81 aa）
Not recorded WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain S 1–81（81 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain S 1–81（81 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain S 1–81（81 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain S 1–81（81 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain S 1–81（81 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain S 1–81（81 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain e 1–81（81 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name VA0E1_HUMAN
Isoform —
PDB entities 12
Chains and sequence ranges Author chain m； PDBConstruct 1–81； UniProt 1–81

Ribonuclease kappa

OrganismNot specified

UniProt Q6P5S7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain n； UniProt 1–137 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain T 1–137（137 aa）
Not recorded WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain T 1–137（137 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain T 1–137（137 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain T 1–137（137 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain T 1–137（137 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain T 1–137（137 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain T 1–137（137 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain f 1–137（137 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name RNK_HUMAN
Isoform —
PDB entities 13
Chains and sequence ranges Author chain n； PDBConstruct 1–137； UniProt 1–137

V-type proton ATPase subunit S1

OrganismNot specified

UniProt Q15904

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain s； UniProt 1–470 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain U 1–470（470 aa）
Not recorded WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain U 1–470（470 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain U 1–470（470 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain U 1–470（470 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain U 1–470（470 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain U 1–470（470 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain U 1–470（470 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain o 1–470（470 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name VAS1_HUMAN
Isoform —
PDB entities 14
Chains and sequence ranges Author chain s； PDBConstruct 1–470； UniProt 1–470

ATPase H(+)-transporting lysosomal accessory protein 2

OrganismNot specified

UniProt A0A1B0GVW0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain r； UniProt 1–345 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

View Construct and Data Evidence
UniProt name A0A1B0GVW0_HUMAN
Isoform —
PDB entities 15
Chains and sequence ranges Author chain r； PDBConstruct 1–345； UniProt 1–345

V-type proton ATPase 16 kDa proteolipid subunit

OrganismNot specified

UniProt P27449

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain 0； UniProt 1–155 Chain 2； UniProt 1–155 Chain 3； UniProt 1–155 Chain 4； UniProt 1–155 Chain 5； UniProt 1–155 Chain 6； UniProt 1–155 Chain 7； UniProt 1–155 Chain 8； UniProt 1–155 Chain 9； UniProt 1–155 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 aa）
Not recorded WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 1 1–155（155 aa）
Chain 2 1–155（155 aa）
Chain 3 1–155（155 aa）
Chain 4 1–155（155 aa）
Chain 5 1–155（155 aa）
Chain 6 1–155（155 aa）
Chain 7 1–155（155 aa）
Chain 8 1–155（155 aa）
Chain 9 1–155（155 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain c 1–155（155 aa）
Chain g 1–155（155 aa）
Chain h 1–155（155 aa）
Chain i 1–155（155 aa）
Chain j 1–155（155 aa）
Chain k 1–155（155 aa）
Chain l 1–155（155 aa）
Chain m 1–155（155 aa）
Chain n 1–155（155 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name VATL_HUMAN
Isoform —
PDB entities 16
Chains and sequence ranges Author chain 0； PDBConstruct 1–155； UniProt 1–155 Author chain 2； PDBConstruct 1–155； UniProt 1–155 Author chain 3； PDBConstruct 1–155； UniProt 1–155 Author chain 4； PDBConstruct 1–155； UniProt 1–155 Author chain 5； PDBConstruct 1–155； UniProt 1–155 Author chain 6； PDBConstruct 1–155； UniProt 1–155 Author chain 7； PDBConstruct 1–155； UniProt 1–155 Author chain 8； PDBConstruct 1–155； UniProt 1–155 Author chain 9； PDBConstruct 1–155； UniProt 1–155

V-type proton ATPase 21 kDa proteolipid subunit

OrganismNot specified

UniProt Q99437

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 33 其他Polymer 2 PDB declaration: 33-meric（33） Consistent with protein copy count Chain 1； UniProt 1–205 Not recorded V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） KIAA1609 protein, isoform CRA_a × 1 （D3DUL8） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit H × 1 （Q9UI12） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） ATPase H(+)-transporting lysosomal accessory protein 2 × 1 （A0A1B0GVW0） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） ;alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose × 1 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

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 7UNF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain 0 1–205（205 aa）
Not recorded WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 0 1–205（205 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 0 1–205（205 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 0 1–205（205 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 0 1–205（205 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 0 1–205（205 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 0 1–205（205 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9DET Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor Deposited 2024-08-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain b 1–205（205 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name VATO_HUMAN
Isoform —
PDB entities 17
Chains and sequence ranges Author chain 1； PDBConstruct 1–205； UniProt 1–205

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 7unf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7unf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7unf
Deposition date deposition_date2022-04-10
Structure title titleCryoEM structure of a mEAK7 bound human V-ATPase complex
Keywords keywordsproton transport, mTOR signaling; PROTON TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier81.37 Å
Radius of gyration Rg (electron density) rg_electron82.43 Å
Forward intensity I(0) i012059900000.00
Molecular weight molecular_weight952160.0 kDa
Excluded volume excluded_volume1198800 ų
Envelope volume envelope_volume1989900 ų
Hydration-shell volume shell_volume204850 ų
Envelope diameter envelope_diameter287.5 Å
Shell Rg shell_rg80.57 Å
Envelope Rg envelope_rg78.37 Å
Shape Rg shape_rg82.43 Å
Total Rg total_rg82.44 Å
Total atoms total_atoms66971
Residues n_residues8805
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax221.8 Å
Rg (real space) rg_real78.51 Å
Rg uncertainty (real space) rg_real_error0.85 Å
I(0) (real space) i0_real1.1700e+10
I(0) uncertainty (real space) i0_real_error2.2550e+08
Rg (reciprocal space) rg_reciprocal80.05 Å
I(0) (reciprocal space) i0_reciprocal12010000000.0000
Solution quality estimate total_estimate0.8982
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary81.7 Å
Skewness Skewness skewness0.351
Kurtosis Kurtosis kurtosis-0.561
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha0.3536
Highest regularization parameter α highest_alpha1862000000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.986; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.010
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (22)

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8. Citations (1)

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9. Files and Curves (10)