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9b8o

Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo

Method: ELECTRON MICROSCOPY Dmax: 151.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain H； UniProt 1–247 Not recorded V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain H 1–247（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
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31 Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain H 1–247（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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 1
Chains and sequence ranges Author chain H； PDBConstruct 1–247； UniProt 1–247

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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain P； UniProt 1–463 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics 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 ligand/ion Different experimental conditions Different structure-quality metrics 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
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 2
Chains and sequence ranges Author chain P； 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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain U； UniProt 1–307 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3
Chains and sequence ranges Author chain U； PDBConstruct 1–307； UniProt 1–307

V-type proton ATPase 116 kDa subunit a 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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain a； UniProt 1–826 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric
Chain 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 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 1–838（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 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 1–838（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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 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 1–838（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 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 1–838（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 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 1–838（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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 ligand/ion Different experimental conditions Different structure-quality metrics 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
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31 Different construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 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 experimental conditions 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 4
Chains and sequence ranges Author chain a； PDBConstruct 1–826； UniProt 1–826

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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain b； UniProt 1–205 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics 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 ligand/ion Different experimental conditions Different structure-quality metrics 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
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 5
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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain d； UniProt 1–351 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain d 1–351（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
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 6
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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain e； UniProt 1–81 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics 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 ligand/ion Different experimental conditions Different structure-quality metrics 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
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 7
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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain f； UniProt 5–90 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 8
Chains and sequence ranges Author chain f； PDBConstruct 1–86； UniProt 5–90

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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） 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 ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain g 1–155（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 ligand/ion Different experimental conditions Different structure-quality metrics 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
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 9
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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain p； UniProt 1–350 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） V-type proton ATPase subunit F × 1 （P50408） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain p 1–350（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 ligand/ion Different experimental conditions Different structure-quality metrics 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
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 10
Chains and sequence ranges Author chain p； PDBConstruct 1–350； UniProt 1–350

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 Other combination Heteromer Protein × 19 其他Polymer 9 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain L； UniProt 1–119 Not recorded ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit S1 × 1 （O54715） Synaptophysin × 1 （P07825） V-type proton ATPase 116 kDa subunit a 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） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 9B8O 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics 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
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31 Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions 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
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 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 11
Chains and sequence ranges Author chain L； PDBConstruct 1–119； UniProt 1–119

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 9b8o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9b8o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9b8o
Deposition date deposition_date2024-03-31
Structure title titleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Keywords keywordsMembrane, Synaptic, Complex, 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_guinier45.65 Å
Radius of gyration Rg (electron density) rg_electron44.31 Å
Forward intensity I(0) i01311860000.00
Molecular weight molecular_weight346620.0 kDa
Excluded volume excluded_volume452580 ų
Envelope volume envelope_volume571910 ų
Hydration-shell volume shell_volume100780 ų
Envelope diameter envelope_diameter160.3 Å
Shell Rg shell_rg53.13 Å
Envelope Rg envelope_rg45.06 Å
Shape Rg shape_rg44.38 Å
Total Rg total_rg44.38 Å
Total atoms total_atoms24407
Residues n_residues3028
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 dmax151.6 Å
Rg (real space) rg_real45.52 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real1.3120e+09
I(0) uncertainty (real space) i0_real_error2.6310e+07
Rg (reciprocal space) rg_reciprocal45.65 Å
I(0) (reciprocal space) i0_reciprocal1312000000.0000
Solution quality estimate total_estimate0.8637
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.3 Å
Skewness Skewness skewness0.311
Kurtosis Kurtosis kurtosis-0.216
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha109800000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.843
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (19)

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8. Citations (1)

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9. Files and Curves (10)