6xby

Cryo-EM structure of V-ATPase from bovine brain, state 2

Method: ELECTRON MICROSCOPY D_max: 217.6 Å Quality: EXCELLENT

▼

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

V-type proton ATPase catalytic 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 × 30 PDB declaration: 30-meric（30） 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 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 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 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain A 1–617（617 aa） Chain B 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
7UNE The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain L 1–617（617 aa） Chain M 1–617（617 aa） Chain N 1–617（617 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å

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

View Construct and Data Evidence

UniProt name	VATA_BOVIN
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 P31408

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain D； UniProt 1–511 Chain E； UniProt 1–511 Chain F； UniProt 1–511	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain D 1–511（511 aa） Chain E 1–511（511 aa） Chain F 1–511（511 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
7UNE The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain O 1–511（511 aa） Chain P 1–511（511 aa） Chain Q 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 3.73 Å

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

View Construct and Data Evidence

UniProt name	VATB2_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–511； UniProt 1–511 Author chain E； PDBConstruct 1–511； UniProt 1–511 Author chain F； PDBConstruct 1–511； UniProt 1–511

V-type proton ATPase subunit C 1

OrganismNot specified

UniProt P21282

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain G； UniProt 1–382	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain G 1–382（382 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain G 1–382（382 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATC1_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–382； UniProt 1–382

V-type proton ATPase subunit D

OrganismNot specified

UniProt A0A3Q1M4W9

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain H； UniProt 1–247	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain H 1–247（247 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain H 1–247（247 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
7UNE The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain D 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 3.73 Å

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

View Construct and Data Evidence

UniProt name	A0A3Q1M4W9_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit E 1

OrganismNot specified

UniProt P11019

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 × 30 PDB declaration: 30-meric（30） 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 catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain I 1–226（226 aa） Chain J 1–226（226 aa） Chain K 1–226（226 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
7UNE The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain b 1–226（226 aa） Chain c 1–226（226 aa） Chain d 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 3.73 Å

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

View Construct and Data Evidence

UniProt name	VATE1_BOVIN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–226； UniProt 1–226 Author chain J； PDBConstruct 1–226； UniProt 1–226 Author chain K； PDBConstruct 1–226； UniProt 1–226

V-type proton ATPase subunit F

OrganismNot specified

UniProt Q28029

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain L； UniProt 1–119	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain L 1–119（119 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain L 1–119（119 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATF_BOVIN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain L； PDBConstruct 1–119； UniProt 1–119

V-type proton ATPase subunit G

OrganismNot specified

UniProt Q0VCV6

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 × 30 PDB declaration: 30-meric（30） 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 catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain M 1–118（118 aa） Chain N 1–118（118 aa） Chain O 1–118（118 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
7UNE The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain e 1–118（118 aa） Chain f 1–118（118 aa） Chain g 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 3.73 Å

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

View Construct and Data Evidence

UniProt name	Q0VCV6_BOVIN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain M； PDBConstruct 1–118； UniProt 1–118 Author chain N； PDBConstruct 1–118； UniProt 1–118 Author chain O； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase subunit H

OrganismNot specified

UniProt F1MZL6

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain P； UniProt 1–465	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain P 1–465（465 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain P 1–465（465 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F1MZL6_BOVIN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain P； PDBConstruct 1–465； UniProt 1–465

V-type proton ATPase subunit a

OrganismNot specified

UniProt F1MJV0

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain a； UniProt 1–838	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain a 1–838（838 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain a 1–838（838 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F1MJV0_BOVIN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain a； PDBConstruct 1–838； UniProt 1–838

V-type proton ATPase 21 kDa proteolipid subunit

OrganismNot specified

UniProt Q2TA24

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain b； UniProt 1–205	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain b 1–205（205 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain b 1–205（205 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATO_BOVIN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain b； PDBConstruct 1–205； UniProt 1–205

V-type proton ATPase subunit d 1

OrganismNot specified

UniProt P61420

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain d； UniProt 1–351	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain d 1–351（351 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain d 1–351（351 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VA0D1_BOVIN
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain d； PDBConstruct 1–351； UniProt 1–351

V-type proton ATPase 16 kDa proteolipid subunit

OrganismNot specified

UniProt P23956

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain c； UniProt 1–155 Chain g； UniProt 1–155 Chain k； UniProt 1–155 Chain l； UniProt 1–155 Chain m； UniProt 1–155 Chain n； UniProt 1–155 Chain o； UniProt 1–155 Chain p； UniProt 1–155 Chain q； UniProt 1–155	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase subunit S1 × 1 （P40682） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain c 1–155（155 aa） Chain g 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa） Chain p 1–155（155 aa） Chain q 1–155（155 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain c 1–155（155 aa） Chain g 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa） Chain p 1–155（155 aa） Chain q 1–155（155 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATL_BOVIN
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain c； PDBConstruct 1–155； UniProt 1–155 Author chain g； PDBConstruct 1–155； UniProt 1–155 Author chain k； PDBConstruct 1–155； UniProt 1–155 Author chain l； PDBConstruct 1–155； UniProt 1–155 Author chain m； PDBConstruct 1–155； UniProt 1–155 Author chain n； PDBConstruct 1–155； UniProt 1–155 Author chain o； PDBConstruct 1–155； UniProt 1–155 Author chain p； PDBConstruct 1–155； UniProt 1–155 Author chain q； PDBConstruct 1–155； UniProt 1–155

V-type proton ATPase subunit S1

OrganismNot specified

UniProt P40682

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain s； UniProt 1–468	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） Renin receptor × 1 （P81134） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain s 1–468（468 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain s 1–468（468 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAS1_BOVIN
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain s； PDBConstruct 1–468； UniProt 1–468

Renin receptor

OrganismNot specified

UniProt P81134

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 × 30 PDB declaration: 30-meric（30） Consistent with protein copy count	Chain r； UniProt 1–351	Not recorded	V-type proton ATPase catalytic subunit A × 3 （P31404） V-type proton ATPase subunit B, brain isoform × 3 （P31408） V-type proton ATPase subunit C 1 × 1 （P21282） V-type proton ATPase subunit D × 1 （A0A3Q1M4W9） V-type proton ATPase subunit E 1 × 3 （P11019） V-type proton ATPase subunit F × 1 （Q28029） V-type proton ATPase subunit G × 3 （Q0VCV6） V-type proton ATPase subunit H × 1 （F1MZL6） V-type proton ATPase subunit a × 1 （F1MJV0） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q2TA24） V-type proton ATPase subunit d 1 × 1 （P61420） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P23956） V-type proton ATPase subunit S1 × 1 （P40682） MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XBY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XBW Cryo-EM structure of V-ATPase from bovine brain, state 1 Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain r 1–351（351 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 OLA OLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7KHR Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Deposited 2020-10-21	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 32-meric	Chain r 1–351（351 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 OLA OLEIC ACID × 1 WEV (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RENR_BOVIN
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain r； PDBConstruct 1–351； UniProt 1–351

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6xby
Deposition date deposition_date	2020-06-07
Structure title title	Cryo-EM structure of V-ATPase from bovine brain, state 2
Keywords keywords	PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	79.81 Å
Radius of gyration Rg (electron density) rg_electron	80.98 Å
Forward intensity I(0) i0	9026650000.00
Molecular weight molecular_weight	817500.0 kDa
Excluded volume excluded_volume	1027000 Å³
Envelope volume envelope_volume	1681200 Å³
Hydration-shell volume shell_volume	178020 Å³
Envelope diameter envelope_diameter	283.1 Å
Shell Rg shell_rg	77.84 Å
Envelope Rg envelope_rg	76.94 Å
Shape Rg shape_rg	80.96 Å
Total Rg total_rg	81.01 Å
Total atoms total_atoms	57516
Residues n_residues	7765
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

▼

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

Maximum dimension Dmax dmax	217.6 Å
Rg (real space) rg_real	76.29 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	8.6600e+09
I(0) uncertainty (real space) i0_real_error	1.5970e+08
Rg (reciprocal space) rg_reciprocal	78.06 Å
I(0) (reciprocal space) i0_reciprocal	8983000000.0000
Solution quality estimate total_estimate	0.9162
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	76.2 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.652
Angular range angular_range	— – 0.1000 Å⁻¹
Current regularization parameter α current_alpha	0.7912
Highest regularization parameter α highest_alpha	2167000000.0000
Real-space data points n_real_points	21
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.003

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase catalytic subunit A
Molecular weight formula_weight	68420.9 kDa
EC 编号 ec_number	7.1.2.2
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	57516

MDFSKLPKIRDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDVKWDFTPCKNLRVGSHITGGDIYGIVNENSLIKHKIMLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGIKEKFSMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKITWSIIREHMGEILYKLSSMKFKDPVKDGEAKIKADYAQLLEDMQNAFRSLED

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit B, brain isoform
Molecular weight formula_weight	56637.6 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

MALRAMRGIVNGAAPELPVPTSGPLAGSREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFERNFIAQGPYENRTVYETLDIGWQLLRIFPKEMLKRIPQSTLSEFYPRDSAKH

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit C 1
Molecular weight formula_weight	44042.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MTEFWLISAPGEKTCQQTWEKLHAATTKNNNLAVSSKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVVKKVAQYMADVLEDSKDKVQENLLANGVDLVTYITRFQWDMAKYPIKQSLKNISEIIAKGVTQIDNDLKSRASAYNNLKGNLQNLERKNAGSLLTRSLAEIVKKDDFVLDSEYLVTLLVVVPKLNHNDWIKQYETLAEMVVPRSSNVLSEDQDSYLCNVTLFRKAVDDFRHKARENKFIVRDFQYNEEEMKADKEEMNRLSTDKKKQFGPLVRWLKVNFSEAFIAWIHVKALRVFVESVLRYGLPVNFQAMLLQPNKKTMKKLREVLYELYKHLDSSAAAIIDAPMDIPGLNLSQQEYYPYVYYKIDCNLLEFK

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit D
Molecular weight formula_weight	28297.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKSDKDLEQRRAAGEVIEPANLLAEEKDEDLLFE

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit E 1
Molecular weight formula_weight	26178.4 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

MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPVYKVATKRDVDVQIDQEAYLPEEIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase subunit F
Molecular weight formula_weight	13417.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MAGRGKLIAVIGDEDTVTGFLLGGIGELNKNRHPNFLVVEKDTTINEIEDTFRQFLNRDDIGIILINQYIAEMVRHALDAHQRSIPAVLEIPSKEHPYDAAKDSILRRARGMFTAEDLR

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit G
Molecular weight formula_weight	13588.3 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

MASQSQGIQQLLQAEKRAAEKVADARKRKARRLKQAKEEAQMEVDQYRREREQEFQSKQQAAMGSQGNLSAEVEQATRRQVQGMQSSQQRNRERVLAQLLGMVCDVRPQVHPNYRIAA

Entity 8 Entity 8 polymer

Description description	V-type proton ATPase subunit H
Molecular weight formula_weight	54155.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MTKMDIRGAVDAAVPTNIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEGSQCAKTFINLMTHISKEQTVQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTVHMAARIIAKLAAWGKELMEGSDLNYYFNWIKTQLSSQSSQYVQCVAGCLQLMLRVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKEKVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYDDEDISEDIKFLLEKLGESVQDLSSFDEYSSELKSGRLEWSPVHKSEKFWRENAARLNEKNYELLKILTKLLEVSDDPQVLAVAAHDVGEYVRHYPRGKRVIEQLGGKQLVMNHMHHEDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS

Entity 9 Entity 9 polymer

Description description	V-type proton ATPase subunit a
Molecular weight formula_weight	96431.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MGELFRSEEMTLAQLFLQSEAAYCCVSELGELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLEESSSLLEPSEMGRGTPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTYGFQNIVDAYGIGTYREINPAPYTIITFPFLFAVMFGDLGHGILMTLFAVWMVLRESRILSQKNENEMFSTIFSGRYIILLMGVFSIYTGLIYNDCFSKSLNIFGSSWSVRPMFDIYNWTEETLRGNPVLQLNPAVTGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHTYFKKPLNIYFGFIPEIIFMTSLFGYLVILIFYKWTAYNAKTSEKAPSLLIHFINMFLFSYGDSGNSMLYSGQKGIQCFLVVVALLCVPWMLLFKPLVLRRQYLRRKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDAEEPTEDEVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLKVKSLAGGLALFFIFAAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYSGTGFKFLPFSFEHIREGKFDD

Entity 10 Entity 10 polymer

Description description	V-type proton ATPase 21 kDa proteolipid subunit
Molecular weight formula_weight	21530.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

MTGLVLLYSGVFVAFWACLLVVGICYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGGVKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATDPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMGD

Entity 11 Entity 11 polymer

Description description	V-type proton ATPase subunit d 1
Molecular weight formula_weight	40369.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MSFFPELYFNVDNGYLEGLVRGLKAGVLSQADYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVIDDRLKEKMVVEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQRSIAELVPKCHPLGSFEQMEAVNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDEMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCPILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGRLYPEGLAQLARADDYEQVKNVADYYPEYKLLFEGAGSNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVKLKEQECRNIVWIAECIAQRHRAKIDNYIPIF

Entity 12 Entity 12 polymer

Description description	V-type proton ATPase 16 kDa proteolipid subunit
Molecular weight formula_weight	15727.7 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	q,p,c,g,k,l,m,n,o

MSEAKNGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEMIMKSIIPVVMAGIIAIYGLVVAVLIANSLNDGISLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK

Entity 13 Entity 13 polymer

Description description	V-type proton ATPase subunit S1
Molecular weight formula_weight	51818.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	s

MMAATAAAQVRAGTRWAPALCRMPWLPLMLVAAAAATSEQQVPLVLWSSDRGLWAPAADTHEGHITSDMQLSTYLDPALELGPRNVLLFLQDKLSIEDFTAYGGVFGNKQDSAFSNLENALDLAPSSLVLPAVDWYAISTLTTYLQEKLGASPLHVDLATLQELKLNASIPALLLIRLPYTASSGLMAPKEVLMGNDEVIGQVLSTLKSEDIPYTAALTAVRPSRVARDVAMVTGGLGRQLLQRTVVPPTMNVPVSYNDSYDTRILFWAQNFSVAYGEHWEDLTSRTFGVQDLNLTGSFWNDTVARLVLTYDSLFGTMVTFKFILANSYYSVSARHWFTLENLEIHSNGSVAYFNASQVTGPSIYSFHCEHVSSENEDGNLLVPDTQPSLWQMTFRDFQIQAFNVTDKKFSYASDCAGFFSPGIWMGLLTSLFMLFIFTYGLHMILSLKTMDRFDDHKGPTITLTQIV

Entity 14 Entity 14 polymer

Description description	Renin receptor
Molecular weight formula_weight	39529.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	r

MAVLVVFLSFLVADVFGNEFSILRSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATVMVMVKGVDKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTLRQLRNRLFQENSVLTSLPLNSLSRNNEVDLLFLSELQVLRDISSLLSRHKHLAKDHSPDLYSLELAGLDEIGKHYGEDSEQFRDASKILIDALQKFADDMYNLYGGNAVVELVTVRSFDTSLVRKTRNILETKQVKDPSTTYNLAYKYNFEYPVVFNLVLWIMIGLALTLIVTCYNIWNMDPGYDSIIYRMTNQKIRMD

Entity 15 Entity 15 non-polymer

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

Entity 16 Entity 16 non-polymer

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

Entity 17 Entity 17 non-polymer

Description description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	760.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 18 Entity 18 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6xbyH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3240 —

Domain ID domain_id	6xbyI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	6xbyJ01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

Domain ID domain_id	6xbyK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	30 — ATP synthase, E subunit, C-terminal

▶

8. Citations (1)

▶

Resolution resolution	3.79 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	41821

fit	/app/data/saxs_computation/xb/6xby/6xby.fit
pddf	/app/data/pr_computation/xb/6xby/6xby.pr.out
profile	/app/data/saxs_computation/xb/6xby/6xby.dat

Cryo-EM structure of V-ATPase from bovine brain, state 2

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

V-type proton ATPase catalytic 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

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 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 F

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 subunit H

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit a

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase 21 kDa proteolipid subunit

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit d 1

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase 16 kDa proteolipid subunit

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase subunit S1

State in the Current Structure

Other States of the Same Protein in the Database

Renin receptor

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (18)

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

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 polymer

Polymer Polymer

Entity 11 Entity 11 polymer

Polymer Polymer

Entity 12 Entity 12 polymer

Polymer Polymer

Entity 13 Entity 13 polymer

Polymer Polymer

Entity 14 Entity 14 polymer

Polymer Polymer