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9brc

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2

Method: ELECTRON MICROSCOPY Dmax: 216.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

H(+)-transporting two-sector ATPase

OrganismNot specified

UniProt D4A133

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain A； UniProt 1–647 Chain B； UniProt 1–647 Chain C； UniProt 1–647 Not recorded V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-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 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 A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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-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 Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-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
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 A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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-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 A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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-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 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
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
7UZF Rat Kidney V-ATPase with SidK, 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 × 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 aa）
Not recorded 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 aa）
Not recorded 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 ligand/ion Different experimental conditions 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 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 A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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 A 1–617（617 aa）
Chain B 1–617（617 aa）
Chain C 1–617（617 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain A 1–647（647 aa）
Chain B 1–647（647 aa）
Chain C 1–647（647 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 1–647（647 aa）
Chain B 1–647（647 aa）
Chain C 1–647（647 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 1–646（646 aa）
Chain B 1–646（646 aa）
Chain C 1–646（646 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

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

View Construct and Data Evidence
UniProt name D4A133_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–647； UniProt 1–647 Author chain B； PDBConstruct 1–647； UniProt 1–647 Author chain C； PDBConstruct 1–647； UniProt 1–647

V-type proton ATPase subunit B, brain isoform

OrganismNot specified

UniProt P62815

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain D； UniProt 1–511 Chain E； UniProt 1–511 Chain F； UniProt 1–511 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-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 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
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
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded 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 ligand/ion Different experimental conditions 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
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 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain D 1–511（511 aa）
Chain E 1–511（511 aa）
Chain F 1–511（511 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination 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 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

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

View Construct and Data Evidence
UniProt name VATB2_RAT
Isoform —
PDB entities 2
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

V-type proton ATPase subunit C 1

OrganismNot specified

UniProt Q5FVI6

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain G； UniProt 1–382 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain G 1–382（382 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain G 1–382（382 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain G 1–382（382 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
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–382（382 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–382（382 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–382（382 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–382（382 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–382（382 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–382（382 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain G 1–382（382 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain G 1–382（382 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain G 1–382（382 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
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–382（382 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain G 1–382（382 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain G 1–382（382 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

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

View Construct and Data Evidence
UniProt name VATC1_RAT
Isoform —
PDB entities 3
Chains and sequence ranges Author chain G； PDBConstruct 1–382； UniProt 1–382

ATPase H+-transporting V1 subunit D

OrganismNot specified

UniProt Q6P503

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain H； UniProt 1–247 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain H 1–247（247 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain H 1–247（247 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain H 1–247（247 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H 1–247（247 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H 1–247（247 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H 1–247（247 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–247（247 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–247（247 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–247（247 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain H 1–247（247 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain H 1–247（247 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain H 1–247（247 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain H 1–247（247 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain H 1–247（247 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain H 1–247（247 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
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain H 1–247（247 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain H 1–247（247 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain H 1–247（247 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain H 1–247（247 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

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

View Construct and Data Evidence
UniProt name Q6P503_RAT
Isoform —
PDB entities 4
Chains and sequence ranges Author chain H； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit E 1

OrganismNot specified

UniProt Q6PCU2

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain I； UniProt 1–226 Chain J； UniProt 1–226 Chain K； UniProt 1–226 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 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 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain I 1–226（226 aa）
Chain J 1–226（226 aa）
Chain K 1–226（226 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

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

View Construct and Data Evidence
UniProt name VATE1_RAT
Isoform —
PDB entities 5
Chains and sequence ranges Author chain I； PDBConstruct 1–226； UniProt 1–226 Author chain J； PDBConstruct 1–226； UniProt 1–226 Author chain K； PDBConstruct 1–226； UniProt 1–226

V-type proton ATPase subunit F

OrganismNot specified

UniProt P50408

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain L； UniProt 1–119 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain L 1–119（119 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain L 1–119（119 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain L 1–119（119 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain L 1–119（119 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain L 1–119（119 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain L 1–119（119 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain L 1–119（119 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain L 1–119（119 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain L 1–119（119 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain L 1–119（119 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain L 1–119（119 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain L 1–119（119 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
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain L 1–119（119 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain L 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 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain L 1–119（119 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain L 1–119（119 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

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATF_RAT
Isoform —
PDB entities 6
Chains and sequence ranges Author chain L； PDBConstruct 1–119； UniProt 1–119

V-type proton ATPase subunit G

OrganismNot specified

UniProt Q8R2H0

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain M； UniProt 1–118 Chain N； UniProt 1–118 Chain O； UniProt 1–118 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain M 1–118（118 aa）
Chain N 1–118（118 aa）
Chain O 1–118（118 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

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8R2H0_RAT
Isoform —
PDB entities 7
Chains and sequence ranges Author chain M； PDBConstruct 1–118； UniProt 1–118 Author chain N； PDBConstruct 1–118； UniProt 1–118 Author chain O； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase subunit S1

OrganismNot specified

UniProt O54715

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain P； UniProt 1–463 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain c 1–463（463 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain c 1–463（463 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain c 1–463（463 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain c 1–463（463 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain c 1–463（463 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain c 1–463（463 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain c 1–463（463 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain c 1–463（463 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain c 1–463（463 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain c 1–463（463 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
8XLI Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus Deposited 2023-12-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain c 248–451（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain P 1–463（463 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain P 1–463（463 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain P 1–463（463 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

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VAS1_RAT
Isoform —
PDB entities 8
Chains and sequence ranges Author chain P； PDBConstruct 1–463； UniProt 1–463

Type IV secretion protein Dot

Legionella pneumophila subsp. pneumophila

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain Q； UniProt 1–573 Chain R； UniProt 1–573 Chain S； UniProt 1–573 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 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 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 experimental conditions 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
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 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 3.40 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01 Different ligand/ion Different experimental conditions 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 experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–337（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–337（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–337（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–280（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–278（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain Q 1–278（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 ligand/ion Different experimental conditions 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 experimental conditions 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 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion 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 9
Chains and sequence ranges Author chain Q； PDBConstruct 1–573； UniProt 1–573 Author chain R； PDBConstruct 1–573； UniProt 1–573 Author chain S； PDBConstruct 1–573； UniProt 1–573

V-type proton ATPase subunit H

OrganismNot specified

UniProt A0A8I5ZQ24

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain T； UniProt 1–463 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain T 1–483（483 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain T 1–463（463 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain T 1–463（463 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8I5ZQ24_RAT
Isoform —
PDB entities 10
Chains and sequence ranges Author chain T； PDBConstruct 1–463； UniProt 1–463

Synaptophysin

OrganismNot specified

UniProt P07825

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain U； UniProt 1–307 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain U 1–307（307 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain U 1–307（307 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain U 1–307（307 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYPH_RAT
Isoform —
PDB entities 11
Chains and sequence ranges Author chain U； PDBConstruct 1–307； UniProt 1–307

V-type proton ATPase 116 kDa subunit a isoform 1

OrganismNot specified

UniProt P25286

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain a； UniProt 1–838 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain a 1–838（838 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain a 1–838（838 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain a 1–838（838 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain a 1–838（838 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain a 1–838（838 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain a 1–838（838 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain a 1–838（838 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
8XLI Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus Deposited 2023-12-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain a 4–831（828 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain a 1–826（826 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain a 1–838（838 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain a 1–832（832 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

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

View Construct and Data Evidence
UniProt name VPP1_RAT
Isoform —
PDB entities 12
Chains and sequence ranges Author chain a； PDBConstruct 1–838； UniProt 1–838

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

OrganismNot specified

UniProt B0K022

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain b； UniProt 1–205 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain b 1–205（205 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain b 1–205（205 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain b 1–205（205 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain b 1–205（205 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain b 1–205（205 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain b 1–205（205 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain b 1–205（205 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain b 1–205（205 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain b 1–205（205 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain b 1–205（205 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
8XLI Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus Deposited 2023-12-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain b 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain b 1–205（205 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain b 1–205（205 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain b 1–205（205 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

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B0K022_RAT
Isoform —
PDB entities 13
Chains and sequence ranges Author chain b； PDBConstruct 1–205； UniProt 1–205

V-type proton ATPase subunit

OrganismNot specified

UniProt Q5M7T6

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain d； UniProt 1–351 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain d 1–351（351 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain d 1–351（351 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain d 1–351（351 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain d 1–351（351 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain d 1–351（351 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain d 1–351（351 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain d 1–351（351 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain d 1–351（351 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain d 1–351（351 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain d 1–351（351 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
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain d 1–351（351 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain d 1–351（351 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain d 1–351（351 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

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5M7T6_RAT
Isoform —
PDB entities 14
Chains and sequence ranges Author chain d； PDBConstruct 1–351； UniProt 1–351

V-type proton ATPase subunit e 2

OrganismNot specified

UniProt Q5EB76

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain e； UniProt 1–81 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain e 1–81（81 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain e 1–81（81 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain e 1–81（81 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain e 1–81（81 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain e 1–81（81 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain e 1–81（81 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain e 1–81（81 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain e 1–81（81 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain e 1–81（81 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain e 1–81（81 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
8XLI Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus Deposited 2023-12-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain e 3–79（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain e 1–81（81 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain e 1–81（81 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain e 1–81（81 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

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VA0E2_RAT
Isoform —
PDB entities 15
Chains and sequence ranges Author chain e； PDBConstruct 1–81； UniProt 1–81

Rnasek protein

OrganismNot specified

UniProt A0A8J8YMT9

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain f； UniProt 5–98 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain f 5–90（86 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain f 5–98（94 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain f 5–90（86 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8J8YMT9_RAT
Isoform —
PDB entities 16
Chains and sequence ranges Author chain f； PDBConstruct 1–94； UniProt 5–98

V-type proton ATPase 16 kDa proteolipid subunit c

OrganismNot specified

UniProt P63081

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain g； UniProt 1–155 Chain h； UniProt 1–155 Chain i； UniProt 1–155 Chain j； UniProt 1–155 Chain k； UniProt 1–155 Chain l； UniProt 1–155 Chain m； UniProt 1–155 Chain n； UniProt 1–155 Chain o； UniProt 1–155 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） Renin receptor × 1 （Q6AXS4） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
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）
Chain o 1–155（155 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
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）
Chain o 1–155（155 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
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）
Chain o 1–155（155 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
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）
Chain o 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
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）
Chain o 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
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）
Chain o 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain g 1–155（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）
Chain o 1–155（155 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain g 1–155（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）
Chain o 1–155（155 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain g 1–155（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）
Chain o 1–155（155 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
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）
Chain o 1–155（155 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
8XLI Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus Deposited 2023-12-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain g 6–155（150 aa）
Chain h 6–155（150 aa）
Chain i 6–155（150 aa）
Chain j 6–155（150 aa）
Chain k 6–155（150 aa）
Chain l 6–155（150 aa）
Chain m 6–155（150 aa）
Chain n 6–155（150 aa）
Chain o 6–155（150 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
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）
Chain o 1–155（155 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
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）
Chain o 1–155（155 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
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）
Chain o 1–155（155 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

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATL_RAT
Isoform —
PDB entities 17
Chains and sequence ranges Author chain g； PDBConstruct 1–155； UniProt 1–155 Author chain h； PDBConstruct 1–155； UniProt 1–155 Author chain i； PDBConstruct 1–155； UniProt 1–155 Author chain j； PDBConstruct 1–155； UniProt 1–155 Author chain k； PDBConstruct 1–155； UniProt 1–155 Author chain l； PDBConstruct 1–155； UniProt 1–155 Author chain m； PDBConstruct 1–155； UniProt 1–155 Author chain n； PDBConstruct 1–155； UniProt 1–155 Author chain o； PDBConstruct 1–155； UniProt 1–155

Renin receptor

OrganismNot specified

UniProt Q6AXS4

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain p； UniProt 1–350 Not recorded H(+)-transporting two-sector ATPase × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit C 1 × 1 （Q5FVI6） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit F × 1 （P50408） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase subunit S1 × 1 （O54715） Type IV secretion protein Dot × 3 （Q5ZWW6） V-type proton ATPase subunit H × 1 （A0A8I5ZQ24） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 （Q5M7T6） V-type proton ATPase subunit e 2 × 1 （Q5EB76） Rnasek protein × 1 （A0A8J8YMT9） V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 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 9BRC 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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain p 1–350（350 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-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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain p 1–350（350 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-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 oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain p 1–350（350 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
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain p 1–350（350 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain p 1–350（350 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain p 1–350（350 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain p 1–350（350 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain p 1–350（350 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain p 1–350（350 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 ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain p 1–350（350 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
8XLI Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus Deposited 2023-12-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain p 292–340（49 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain p 1–350（350 aa）
Not recorded PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 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 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain p 1–350（350 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
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain p 1–350（350 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

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RENR_RAT
Isoform —
PDB entities 18
Chains and sequence ranges Author chain p； PDBConstruct 1–350； UniProt 1–350

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 9brc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9brc
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9brc
Deposition date deposition_date2024-05-11
Structure title titleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 2
Keywords keywordsSynaptic, vesicle, membrane, PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier83.30 Å
Radius of gyration Rg (electron density) rg_electron83.53 Å
Forward intensity I(0) i08828510000.00
Molecular weight molecular_weight650130.0 kDa
Excluded volume excluded_volume747480 ų
Envelope volume envelope_volume1837400 ų
Hydration-shell volume shell_volume186400 ų
Envelope diameter envelope_diameter281.3 Å
Shell Rg shell_rg80.64 Å
Envelope Rg envelope_rg79.19 Å
Shape Rg shape_rg83.53 Å
Total Rg total_rg83.48 Å
Total atoms total_atoms46442
Residues n_residues9424
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 dmax216.7 Å
Rg (real space) rg_real80.28 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real8.5640e+09
I(0) uncertainty (real space) i0_real_error1.6050e+08
Rg (reciprocal space) rg_reciprocal82.12 Å
I(0) (reciprocal space) i0_reciprocal8798000000.0000
Solution quality estimate total_estimate0.8950
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary91.2 Å
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.736
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha0.1272
Highest regularization parameter α highest_alpha1433000000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.001
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (18)

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8. Citations (1)

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9. Files and Curves (10)