SAXSdb — 6vqa

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATPase H+-transporting V1 subunit A

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–617 Chain B； UniProt 1–617 Chain C； UniProt 1–617	Not recorded	V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） Effector protein SidK × 3 （Q5ZWW6） 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

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 6VQA	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain A 1–647（647 aa） Chain B 1–647（647 aa） Chain C 1–647（647 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different 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 1–647（647 aa） Chain B 1–647（647 aa） Chain C 1–647（647 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
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 1–647（647 aa） Chain B 1–647（647 aa） Chain C 1–647（647 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 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 1–646（646 aa） Chain B 1–646（646 aa） Chain C 1–646（646 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	D4A133_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–617； UniProt 1–617 Author chain B； PDBConstruct 1–617； UniProt 1–617 Author chain C； PDBConstruct 1–617； UniProt 1–617

V-type proton ATPase subunit B, brain isoform

OrganismNot specified

UniProt P62815

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain D； UniProt 1–511 Chain E； UniProt 1–511 Chain F； UniProt 1–511	Not recorded	ATPase H+-transporting V1 subunit A × 3 （D4A133） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） Effector protein SidK × 3 （Q5ZWW6） 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

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 6VQA	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	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 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 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 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	VATB2_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–511； UniProt 1–511 Author chain E； PDBConstruct 1–511； UniProt 1–511 Author chain F； PDBConstruct 1–511； UniProt 1–511

ATPase H+-transporting V1 subunit D

OrganismNot specified

UniProt Q6P503

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain H； UniProt 1–247	Not recorded	ATPase H+-transporting V1 subunit A × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） Effector protein SidK × 3 （Q5ZWW6） 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

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 6VQA	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 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 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 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 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
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 ligand/ion 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 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 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 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 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	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 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 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 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain H 1–247（247 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain H 1–247（247 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain H 1–247（247 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different 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	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit E 1

OrganismNot specified

UniProt Q6PCU2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain I； UniProt 1–226 Chain J； UniProt 1–226 Chain K； UniProt 1–226	Not recorded	ATPase H+-transporting V1 subunit A × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit G × 3 （Q8R2H0） Effector protein SidK × 3 （Q5ZWW6） 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

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 6VQA	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
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 I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 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 I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	VATE1_RAT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain I； PDBConstruct 1–226； UniProt 1–226 Author chain J； PDBConstruct 1–226； UniProt 1–226 Author chain K； PDBConstruct 1–226； UniProt 1–226

V-type proton ATPase subunit G

OrganismNot specified

UniProt Q8R2H0

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain M； UniProt 1–118 Chain N； UniProt 1–118 Chain O； UniProt 1–118	Not recorded	ATPase H+-transporting V1 subunit A × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） Effector protein SidK × 3 （Q5ZWW6） 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

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 6VQA	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
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 M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 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 M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	Q8R2H0_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–118； UniProt 1–118 Author chain N； PDBConstruct 1–118； UniProt 1–118 Author chain O； PDBConstruct 1–118； UniProt 1–118

Effector protein SidK

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

UniProt Q5ZWW6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain Q； UniProt 1–278 Chain R； UniProt 1–278 Chain S； UniProt 1–278	Fragment：N-terminal fragment with 3x FLAG tag	ATPase H+-transporting V1 subunit A × 3 （D4A133） V-type proton ATPase subunit B, brain isoform × 3 （P62815） ATPase H+-transporting V1 subunit D × 1 （Q6P503） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） 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

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 6VQA	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ9 Mammalian V-ATPase from rat brain soluble V1 region rotational state 1 with SidK and ADP (from focused refinement) Deposited 2020-02-04	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain Q 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain R 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag Chain S 1–278（278 aa） Fragment：N-terminal fragment with 3x FLAG tag	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
6VQB Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement) Deposited 2020-02-04	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain Q 1–278（278 aa） Chain R 1–278（278 aa） Chain S 1–278（278 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.60 Å
6WLZ The V1 region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain X 1–573（573 aa） Chain Y 1–573（573 aa） Chain Z 1–573（573 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different 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 X 1–573（573 aa） Chain Y 1–573（573 aa） Chain Z 1–573（573 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different 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 X 1–573（573 aa） Chain Y 1–573（573 aa） Chain Z 1–573（573 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U8O Structure of porcine V-ATPase with mEAK7 and SidK, Rotary state 2 Deposited 2022-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain Q 1–337（337 aa） Chain R 1–337（337 aa） Chain S 1–337（337 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7U8P Structure of porcine kidney V-ATPase with SidK, Rotary State 1 Deposited 2022-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–337（337 aa） Chain R 1–337（337 aa） Chain S 1–337（337 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7U8Q Structure of porcine kidney V-ATPase with SidK, Rotary State 2 Deposited 2022-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–337（337 aa） Chain R 1–337（337 aa） Chain S 1–337（337 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7U8R Structure of porcine kidney V-ATPase with SidK, Rotary State 3 Deposited 2022-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–337（337 aa） Chain R 1–337（337 aa） Chain S 1–337（337 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–280（280 aa） Chain R 1–280（280 aa） Chain S 1–280（280 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–278（278 aa） Chain R 1–278（278 aa） Chain S 1–278（278 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–278（278 aa） Chain R 1–278（278 aa） Chain S 1–278（278 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain Q 1–278（278 aa） Chain R 1–278（278 aa） Chain S 1–278（278 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
7UZJ Rat Kidney V1 complex with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain Q 1–280（280 aa） Chain R 1–280（280 aa） Chain S 1–280（280 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain Q 1–280（280 aa） Chain R 1–280（280 aa） Chain S 1–280（280 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain Q 1–573（573 aa） Chain R 1–573（573 aa） Chain S 1–573（573 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain Q 1–573（573 aa） Chain R 1–573（573 aa） Chain S 1–573（573 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain Q 1–573（573 aa） Chain R 1–573（573 aa） Chain S 1–573（573 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different 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 Q 1–573（573 aa） Chain R 1–573（573 aa） Chain S 1–573（573 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	Q5ZWW6_LEGPH
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain Q； PDBConstruct 2–279； UniProt 1–278 Author chain R； PDBConstruct 2–279； UniProt 1–278 Author chain S； PDBConstruct 2–279； UniProt 1–278

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vqa
Deposition date deposition_date	2020-02-04
Structure title title	Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement)
Keywords keywords	membrane protein complex, rotary atpase, PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.70 Å
Radius of gyration Rg (electron density) rg_electron	51.24 Å
Forward intensity I(0) i0	3685830000.00
Molecular weight molecular_weight	514300.0 kDa
Excluded volume excluded_volume	646080 Å³
Envelope volume envelope_volume	877990 Å³
Hydration-shell volume shell_volume	133320 Å³
Envelope diameter envelope_diameter	169.1 Å
Shell Rg shell_rg	60.79 Å
Envelope Rg envelope_rg	51.13 Å
Shape Rg shape_rg	51.23 Å
Total Rg total_rg	51.52 Å
Total atoms total_atoms	36114
Residues n_residues	4578
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	170.2 Å
Rg (real space) rg_real	51.48 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	3.6860e+09
I(0) uncertainty (real space) i0_real_error	6.8040e+07
Rg (reciprocal space) rg_reciprocal	51.87 Å
I(0) (reciprocal space) i0_reciprocal	3688000000.0000
Solution quality estimate total_estimate	0.8749
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.4 Å
Skewness Skewness skewness	0.169
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	756900000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.929

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	ATPase H+-transporting V1 subunit A
Molecular weight formula_weight	68341.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	36114

MDFSKLPKIRDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDIKWEFIPSKNLRVGSHITGGDIYGIVNENSLIKHKIMLPPRSRGSVTYIAPPGNYDASDVVLELEFEGVKEKLSMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMISFYDMARRAVETTAQSDNKITWSIIREHMGEILYKLSSMKFKDPVKDGEAKIKADYAQLLEDMQNAFRSLED

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit B, brain isoform
Molecular weight formula_weight	56611.6 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MALRAMRGIVNGAAPELPVPTGGPMAGAREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFEKNFITQGPYENRTVYETLDIGWQLLRIFPKEMLKRIPQSTLSEFYPRDSAKH

Entity 3 Entity 3 polymer

Description description	ATPase H+-transporting V1 subunit D
Molecular weight formula_weight	28359.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKIIKEKSEKDLERRRAAGEVMEPANLLAEEKDEDLLFE

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit E 1
Molecular weight formula_weight	26167.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K

MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATKKDVDVQIDLEAYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit G
Molecular weight formula_weight	13690.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O

MASQSQGIQQLLQAEKRAAEKVADARKRKARRLKQAKEEAQMEVEQYRREREQEFQSKQQAAMGSQGNLSAEVEQATRRQVQGMQSSQQRNRERVLTQLLGMVCDVRPQVHPNYRITV

Entity 6 Entity 6 polymer

Description description	Effector protein SidK
Molecular weight formula_weight	34693.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,R,S

GMSFIKVGIKMGGLTSEQYHSQVVGKIGYIARCMQTIDPENNLKKIREDYQDVLIWAEKNYRFEEILEASKSGKCPNDLDALSRRSLILQELLRLVSSISPFKMKLDLIESQYEKMKQHVNLWKSDYHVKLNQLNQLTDYLKNAAPTPKNNFLRAMTSVLQMQIAQYGITEDNEGINQLFKLGLHLLAMANEKIDEQYHLFKGYVKDQPEESPFEGILPAEDQKILVKTMIDYAMPKLSSKVLQDKLSALSSSDVLTKTLLDSIDRIVKENEKLNALSKDYKDHDGDYKDHDIDYKDDDDK

来源 Source

来源生物 organism	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	6vqaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6vqaA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6vqaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6vqaB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6vqaC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6vqaC03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6vqaD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	6vqaE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

Domain ID domain_id	6vqaF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12240 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	74789

fit	/app/data/saxs_computation/vq/6vqa/6vqa.fit
pddf	/app/data/pr_computation/vq/6vqa/6vqa.pr.out
profile	/app/data/saxs_computation/vq/6vqa/6vqa.dat

Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement)

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATPase H+-transporting V1 subunit A

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit B, brain isoform

State in the Current Structure

Other States of the Same Protein in the Database

ATPase H+-transporting V1 subunit D

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit E 1

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit G

State in the Current Structure

Other States of the Same Protein in the Database

Effector protein SidK

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)