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6wm3

Human V-ATPase in state 2 with SidK and ADP

Method: ELECTRON MICROSCOPY Dmax: 218.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

V-type proton ATPase 116 kDa subunit a isoform 1

OrganismNot specified

UniProt Q93050

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain R； UniProt 1–837 Not recorded V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain R 1–837（837 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 structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain R 1–837（837 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain R 1–837（837 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain R 1–837（837 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain R 1–837（837 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain R 1–837（837 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

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VPP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain R； PDBConstruct 1–837； UniProt 1–837

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain O； UniProt 1–382 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain C 1–382（382 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å

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 2
Chains and sequence ranges Author chain O； PDBConstruct 1–382； UniProt 1–382

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain H； UniProt 1–226 Chain I； UniProt 1–226 Chain J； UniProt 1–226 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain b 1–226（226 aa）
Chain c 1–226（226 aa）
Chain d 1–226（226 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 3
Chains and sequence ranges Author chain H； PDBConstruct 1–226； UniProt 1–226 Author chain I； PDBConstruct 1–226； UniProt 1–226 Author chain J； 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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain K； UniProt 1–118 Chain L； UniProt 1–118 Chain M； UniProt 1–118 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain e 1–118（118 aa）
Chain f 1–118（118 aa）
Chain g 1–118（118 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 4
Chains and sequence ranges Author chain K； PDBConstruct 1–118； UniProt 1–118 Author chain L； PDBConstruct 1–118； UniProt 1–118 Author chain M； PDBConstruct 1–118； UniProt 1–118

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain S； UniProt 1–81 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain m 1–81（81 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 5
Chains and sequence ranges Author chain S； 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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain T； UniProt 1–137 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain n 1–137（137 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 6
Chains and sequence ranges Author chain T； 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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain U； UniProt 1–470 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain s 1–470（470 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 7
Chains and sequence ranges Author chain U； PDBConstruct 1–470； UniProt 1–470

Renin receptor

OrganismNot specified

UniProt O75787

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain V； UniProt 1–350 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） 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 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LBS Crystal structure of the cytoplasmic tail of (pro)renin receptor as a MBP fusion (Maltose-bound form) Deposited 2010-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350
Chain B 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；28% PEG4000, 0.2M Magnesium Chloride, 0.1 M Cacodylate, pH 6.5, EVAPORATION, temperature 293K
Resolution 2.15 Å R-free 0.278
3LC8 Crystal structure of the cytoplasmic tail of (pro)renin receptor as a MBP fusion (Maltose-free form) Deposited 2010-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350
Chain B 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350
Not recorded PG4 TETRAETHYLENE GLYCOL × 2 GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；20% PEG 4000, 0.2M Magnesium Chloride, 0.1M Tris, pH 8.5, EVAPORATION, temperature 293K
Resolution 2.00 Å R-free 0.257
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain V 1–350（350 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 structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric
Chain V 1–350（350 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain V 1–350（350 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain V 1–350（350 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain V 1–350（350 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain V 1–350（350 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 p 1–350（350 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

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RENR_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain V； PDBConstruct 1–350； UniProt 1–350

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain 0； UniProt 1–205 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain 1 1–205（205 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 9
Chains and sequence ranges Author chain 0； PDBConstruct 1–205； UniProt 1–205

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain 1； 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 isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain 0 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 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
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 10
Chains and sequence ranges Author chain 1； 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 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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain Q； UniProt 1–351 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain k 1–351（351 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 Q； PDBConstruct 1–351； UniProt 1–351

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain A； UniProt 1–617 Chain B； UniProt 1–617 Chain C； UniProt 1–617 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain L 1–617（617 aa）
Chain M 1–617（617 aa）
Chain N 1–617（617 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 12
Chains and sequence ranges Author chain A； PDBConstruct 1–617； UniProt 1–617 Author chain B； PDBConstruct 1–617； UniProt 1–617 Author chain C； 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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain D； UniProt 1–511 Chain E； UniProt 1–511 Chain F； UniProt 1–511 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain O 1–511（511 aa）
Chain P 1–511（511 aa）
Chain Q 1–511（511 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 13
Chains and sequence ranges Author chain D； PDBConstruct 1–511； UniProt 1–511 Author chain E； PDBConstruct 1–511； UniProt 1–511 Author chain F； PDBConstruct 1–511； UniProt 1–511

SidK

OrganismNot specified

UniProt Q5ZWW6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain X； UniProt 1–573 Chain Y； UniProt 1–573 Chain Z； UniProt 1–573 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） 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 F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6VQ9 Mammalian V-ATPase from rat brain soluble V1 region rotational state 1 with SidK and ADP (from focused refinement) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
6VQA Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
6VQB Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain Q 1–278（278 aa）
Chain R 1–278（278 aa）
Chain S 1–278（278 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain X 1–573（573 aa）
Chain Y 1–573（573 aa）
Chain Z 1–573（573 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
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain X 1–573（573 aa）
Chain Y 1–573（573 aa）
Chain Z 1–573（573 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
7U8O Structure of porcine V-ATPase with mEAK7 and SidK, Rotary state 2 Deposited 2022-03-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain Q 1–337（337 aa）
Chain R 1–337（337 aa）
Chain S 1–337（337 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7U8P Structure of porcine kidney V-ATPase with SidK, Rotary State 1 Deposited 2022-03-09 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–337（337 aa）
Chain R 1–337（337 aa）
Chain S 1–337（337 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7U8Q Structure of porcine kidney V-ATPase with SidK, Rotary State 2 Deposited 2022-03-09 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–337（337 aa）
Chain R 1–337（337 aa）
Chain S 1–337（337 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7U8R Structure of porcine kidney V-ATPase with SidK, Rotary State 3 Deposited 2022-03-09 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–337（337 aa）
Chain R 1–337（337 aa）
Chain S 1–337（337 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–280（280 aa）
Chain R 1–280（280 aa）
Chain S 1–280（280 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–278（278 aa）
Chain R 1–278（278 aa）
Chain S 1–278（278 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–278（278 aa）
Chain R 1–278（278 aa）
Chain S 1–278（278 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09 Different construct 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 1–278（278 aa）
Chain R 1–278（278 aa）
Chain S 1–278（278 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7UZJ Rat Kidney V1 complex with SidK and NCOA7B, State 1 Deposited 2022-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain Q 1–280（280 aa）
Chain R 1–280（280 aa）
Chain S 1–280（280 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain Q 1–280（280 aa）
Chain R 1–280（280 aa）
Chain S 1–280（280 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain Q 1–573（573 aa）
Chain R 1–573（573 aa）
Chain S 1–573（573 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 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 1–573（573 aa）
Chain R 1–573（573 aa）
Chain S 1–573（573 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 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 1–573（573 aa）
Chain R 1–573（573 aa）
Chain S 1–573（573 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain Q 1–573（573 aa）
Chain R 1–573（573 aa）
Chain S 1–573（573 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 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 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

22 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5ZWW6_LEGPH
Isoform —
PDB entities 14
Chains and sequence ranges Author chain X； PDBConstruct 1–573； UniProt 1–573 Author chain Y； PDBConstruct 1–573； UniProt 1–573 Author chain Z； PDBConstruct 1–573； UniProt 1–573

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain G； UniProt 1–247 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit F × 1 （Q16864） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain D 1–247（247 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 15
Chains and sequence ranges Author chain G； PDBConstruct 1–247； UniProt 1–247

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain N； UniProt 1–119 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit H × 1 （Q9UI12） 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

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 6WM3 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 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain F 1–119（119 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27 Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 16
Chains and sequence ranges Author chain N； PDBConstruct 1–119； UniProt 1–119

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 Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count Chain P； UniProt 1–483 Not recorded V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （Q93050） V-type proton ATPase subunit C 1 × 1 （P21283） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） 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

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 6WM3 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 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
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20 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 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 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 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain P 1–483（483 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric
Chain H 1–483（483 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å

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

View Construct and Data Evidence
UniProt name VATH_HUMAN
Isoform —
PDB entities 17
Chains and sequence ranges Author chain P； PDBConstruct 1–483； UniProt 1–483

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 6wm3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wm3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wm3
Deposition date deposition_date2020-04-20
Structure title titleHuman V-ATPase in state 2 with SidK and ADP
Keywords keywordsV-ATPase, proton pump, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier83.09 Å
Radius of gyration Rg (electron density) rg_electron84.12 Å
Forward intensity I(0) i013089700000.00
Molecular weight molecular_weight991620.0 kDa
Excluded volume excluded_volume1248000 ų
Envelope volume envelope_volume2080100 ų
Hydration-shell volume shell_volume207480 ų
Envelope diameter envelope_diameter285.9 Å
Shell Rg shell_rg82.95 Å
Envelope Rg envelope_rg79.93 Å
Shape Rg shape_rg84.13 Å
Total Rg total_rg84.06 Å
Total atoms total_atoms69754
Residues n_residues9209
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 dmax218.1 Å
Rg (real space) rg_real79.91 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real1.2660e+10
I(0) uncertainty (real space) i0_real_error2.3040e+08
Rg (reciprocal space) rg_reciprocal81.93 Å
I(0) (reciprocal space) i0_reciprocal13050000000.0000
Solution quality estimate total_estimate0.9073
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary91.8 Å
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.684
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha0.2128
Highest regularization parameter α highest_alpha2138000000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.976; Stabil: 0.981; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.002
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (19)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6wm3G01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily3240 —
Domain ID domain_id6wm3H01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily30 — ATP synthase, E subunit, C-terminal
Domain ID domain_id6wm3I01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily30 — ATP synthase, E subunit, C-terminal
Domain ID domain_id6wm3J01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily30 — ATP synthase, E subunit, C-terminal
Domain ID domain_id6wm3P01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id6wm3P02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily150 — V-type ATPase, subunit H, C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)