SAXSdb — 6vqi

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

V-type proton ATPase subunit C 1

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain G； UniProt 1–382	Not recorded	V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 4.30 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 6VQI	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–382（382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–382（382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
7UZJ Rat Kidney V1 complex with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain G 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 1–382（382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain G 1–382（382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain G 1–382（382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 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 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	VATC1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–382； UniProt 1–382

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain I； UniProt 1–226 Chain J； UniProt 1–226 Chain K； UniProt 1–226	Not recorded	V-type proton ATPase subunit C 1 × 1 （Q5FVI6） V-type proton ATPase subunit G × 3 （Q8R2H0） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 4.30 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 6VQI	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 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 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 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 oligomeric state 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 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
6VQB Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different 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
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	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 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 Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UZK Rat Kidney V1 complex lacking subunit H with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state 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 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	2
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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain M； UniProt 1–118 Chain N； UniProt 1–118 Chain O； UniProt 1–118	Not recorded	V-type proton ATPase subunit C 1 × 1 （Q5FVI6） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase 116 kDa subunit a isoform 1 × 1 （P25286）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 4.30 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 6VQI	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 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 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 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 oligomeric state 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 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
6VQB Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different 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
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
9B8P Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Deposited 2024-03-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state 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 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	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–118； UniProt 1–118 Author chain N； PDBConstruct 1–118； UniProt 1–118 Author chain O； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase 116 kDa subunit a isoform 1

OrganismNot specified

UniProt P25286

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain a； UniProt 1–838	Not recorded	V-type proton ATPase subunit C 1 × 1 （Q5FVI6） V-type proton ATPase subunit E 1 × 3 （Q6PCU2） V-type proton ATPase subunit G × 3 （Q8R2H0）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 4.30 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 6VQI	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 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 oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different oligomeric state Different ligand/ion Different 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 oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different oligomeric state Different 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
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different oligomeric state Different ligand/ion Different 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 oligomeric state Different ligand/ion 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 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
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain a 1–826（826 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different oligomeric state 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 oligomeric state 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 1–838； UniProt 1–838

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	6vqi
Deposition date deposition_date	2020-02-05
Structure title title	Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (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	62.38 Å
Radius of gyration Rg (electron density) rg_electron	62.20 Å
Forward intensity I(0) i0	116502000.00
Molecular weight molecular_weight	73917.0 kDa
Excluded volume excluded_volume	85569 Å³
Envelope volume envelope_volume	263440 Å³
Hydration-shell volume shell_volume	37948 Å³
Envelope diameter envelope_diameter	168.6 Å
Shell Rg shell_rg	62.47 Å
Envelope Rg envelope_rg	55.56 Å
Shape Rg shape_rg	62.18 Å
Total Rg total_rg	62.28 Å
Total atoms total_atoms	5278
Residues n_residues	1062
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	173.0 Å
Rg (real space) rg_real	62.11 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	1.1650e+08
I(0) uncertainty (real space) i0_real_error	2.3660e+06
Rg (reciprocal space) rg_reciprocal	62.52 Å
I(0) (reciprocal space) i0_reciprocal	116600000.0000
Solution quality estimate total_estimate	0.6683
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	110.7 Å
Skewness Skewness skewness	-0.262
Kurtosis Kurtosis kurtosis	-1.087
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5244000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.311; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.752; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase subunit C 1
Molecular weight formula_weight	43958.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	5278

MTEFWLISAPGEKTCQQTWEKLHAATTKNNNLAVSSKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVVKKVAQYMADVLEDSKDKVQENLLASGVDLVTYITRFQWDMAKYPIKQSLKNISEIIAKGVTQIDNDLKSRASAYNNLKGNLQNLERKNAGSLLTRSLAEIVKKDDFVLDSEYLVTLLVVVPKLNHNDWIKQYETLAEMVVPRSSNVLSEDQDSYLCNVTLFKKAVDDFRHKARENKFIVRDFQYNEEEMRADKEEMNRLSTDKKKQFGPLVRWLKVNFSEAFIAWIHIKALRVFVESVLRYGLPVNFQAMLLQPNKKSVKKLREVLHELYKHLDSSAAAIIDAPMDIPGLNLSQQEYYPYVYYKIDCNLLEFK

Entity 2 Entity 2 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 3 Entity 3 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 4 Entity 4 polymer

Description description	V-type proton ATPase 116 kDa subunit a isoform 1
Molecular weight formula_weight	96429.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MGELFRSEEMTLAQLFLQSEAAYCCVSELEELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLEESSSLLEPNEMGRGAPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTHGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGLIYNDCFSKSLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIHFINMFLFSYPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQYLRKKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDAEEPTEDEVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYTGTGFKFLPFSFEHIREGKFDE

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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	4.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	90648

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

Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement)

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

V-type proton ATPase subunit C 1

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

V-type proton ATPase 116 kDa subunit a isoform 1

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 (4)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)