9det

Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor

Method: ELECTRON MICROSCOPY D_max: 159.6 Å Quality: REASONABLE

▼

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

V-type proton ATPase subunit e 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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain e； UniProt 1–81	Not recorded	Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 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 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain S 1–81（81 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain S 1–81（81 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain S 1–81（81 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain S 1–81（81 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain S 1–81（81 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain m 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain S 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain S 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VA0E1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain e； PDBConstruct 1–81； UniProt 1–81

Ribonuclease kappa

OrganismNot specified

UniProt Q6P5S7

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain f； UniProt 1–137	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain T 1–137（137 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain T 1–137（137 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain T 1–137（137 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain T 1–137（137 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain T 1–137（137 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain n 1–137（137 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain T 1–137（137 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain T 1–137（137 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain f； PDBConstruct 1–137； UniProt 1–137

V-type proton ATPase subunit S1

OrganismNot specified

UniProt Q15904

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain o； UniProt 1–470	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain U 1–470（470 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain U 1–470（470 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain U 1–470（470 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain U 1–470（470 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain U 1–470（470 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain s 1–470（470 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain U 1–470（470 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain U 1–470（470 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAS1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain o； PDBConstruct 1–470； UniProt 1–470

Renin receptor

OrganismNot specified

UniProt O75787

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain p； UniProt 1–350	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LBS Crystal structure of the cytoplasmic tail of (pro)renin receptor as a MBP fusion (Maltose-bound form) Deposited 2010-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350 Chain B 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；28% PEG4000, 0.2M Magnesium Chloride, 0.1 M Cacodylate, pH 6.5, EVAPORATION, temperature 293K	Resolution 2.15 Å R-free 0.278
3LC8 Crystal structure of the cytoplasmic tail of (pro)renin receptor as a MBP fusion (Maltose-free form) Deposited 2010-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350 Chain B 332–349（18 aa） Fragment：Maltose-binding periplasmic protein, residues 29-390, Renin receptor, residues 332-350	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 GOL GLYCEROL × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；20% PEG 4000, 0.2M Magnesium Chloride, 0.1M Tris, pH 8.5, EVAPORATION, temperature 293K	Resolution 2.00 Å R-free 0.257
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain V 1–350（350 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain V 1–350（350 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain V 1–350（350 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain V 1–350（350 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain V 1–350（350 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain V 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain V 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RENR_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain p； PDBConstruct 1–350； UniProt 1–350

V-type proton ATPase 21 kDa proteolipid subunit

OrganismNot specified

UniProt Q99437

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain b； UniProt 1–205	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain 0 1–205（205 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 0 1–205（205 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 0 1–205（205 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 0 1–205（205 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain 0 1–205（205 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain 1 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 0 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 0 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATO_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain b； PDBConstruct 1–205； UniProt 1–205

V-type proton ATPase 16 kDa proteolipid subunit

OrganismNot specified

UniProt P27449

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain c； UniProt 1–155 Chain g； UniProt 1–155 Chain h； UniProt 1–155 Chain i； UniProt 1–155 Chain j； UniProt 1–155 Chain k； UniProt 1–155 Chain l； UniProt 1–155 Chain m； UniProt 1–155 Chain n； UniProt 1–155	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase subunit d 1 × 1 （P61421） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain 0 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 1 1–155（155 aa） Chain 2 1–155（155 aa） Chain 3 1–155（155 aa） Chain 4 1–155（155 aa） Chain 5 1–155（155 aa） Chain 6 1–155（155 aa） Chain 7 1–155（155 aa） Chain 8 1–155（155 aa） Chain 9 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATL_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain c； PDBConstruct 1–155； UniProt 1–155 Author chain g； PDBConstruct 1–155； UniProt 1–155 Author chain h； PDBConstruct 1–155； UniProt 1–155 Author chain i； PDBConstruct 1–155； UniProt 1–155 Author chain j； PDBConstruct 1–155； UniProt 1–155 Author chain k； PDBConstruct 1–155； UniProt 1–155 Author chain l； PDBConstruct 1–155； UniProt 1–155 Author chain m； PDBConstruct 1–155； UniProt 1–155 Author chain n； PDBConstruct 1–155； UniProt 1–155

V-type proton ATPase subunit d 1

OrganismNot specified

UniProt P61421

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain d； UniProt 1–351	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase 116 kDa subunit a 4 × 1 （Q9HBG4） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6WLW The Vo region of human V-ATPase in state 1 (focused refinement) Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain Q 1–351（351 aa）	Not recorded	WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 PTY PHOSPHATIDYLETHANOLAMINE × 13 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6WM2 Human V-ATPase in state 1 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–351（351 aa）	Not recorded	CLR CHOLESTEROL × 4 PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 13 WSS tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6WM3 Human V-ATPase in state 2 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–351（351 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6WM4 Human V-ATPase in state 3 with SidK and ADP Deposited 2020-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain Q 1–351（351 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7U4T Human V-ATPase in state 2 with SidK and mEAK-7 Deposited 2022-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain Q 1–351（351 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain k 1–351（351 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9CF8 Cryo-EM structure of human kidney V-ATPase state 1 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain Q 1–351（351 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9CFC Cryo-EM structure of human kidney V-ATPase state 2 Deposited 2024-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain Q 1–351（351 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VA0D1_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain d； PDBConstruct 1–351； UniProt 1–351

V-type proton ATPase 116 kDa subunit a 4

Homo sapiens

UniProt Q9HBG4

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 × 17 PDB declaration: 17-meric（17） Consistent with protein copy count	Chain a； UniProt 1–840	Not recorded	V-type proton ATPase subunit e 1 × 1 （O15342） Ribonuclease kappa × 1 （Q6P5S7） V-type proton ATPase subunit S1 × 1 （Q15904） Renin receptor × 1 （O75787） V-type proton ATPase 21 kDa proteolipid subunit × 1 （Q99437） V-type proton ATPase 16 kDa proteolipid subunit × 9 （P27449） V-type proton ATPase subunit d 1 × 1 （P61421） Anti V-ATPase Nanobody 2CAS66 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 A1A4Q Cladoniamide A × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；20 mM Tris, 150 mM NaCl, 0.5 mM EDTA, 2 mM DTT, pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DET	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7UNF CryoEM structure of a mEAK7 bound human V-ATPase complex Deposited 2022-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain a 1–840（840 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPP4_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain a； PDBConstruct 1–840； UniProt 1–840

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	9det
Deposition date deposition_date	2024-08-29
Structure title title	Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor
Keywords keywords	V-ATPase, lipid nanodisc, Vo subcomplex, inhibitor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	47.61 Å
Radius of gyration Rg (electron density) rg_electron	46.51 Å
Forward intensity I(0) i0	1552310000.00
Molecular weight molecular_weight	356500.0 kDa
Excluded volume excluded_volume	457520 Å³
Envelope volume envelope_volume	628080 Å³
Hydration-shell volume shell_volume	107660 Å³
Envelope diameter envelope_diameter	172.2 Å
Shell Rg shell_rg	54.94 Å
Envelope Rg envelope_rg	45.60 Å
Shape Rg shape_rg	46.39 Å
Total Rg total_rg	47.29 Å
Total atoms total_atoms	50652
Residues n_residues	3209
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	159.6 Å
Rg (real space) rg_real	47.35 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	1.5520e+09
I(0) uncertainty (real space) i0_real_error	2.6110e+07
Rg (reciprocal space) rg_reciprocal	47.61 Å
I(0) (reciprocal space) i0_reciprocal	1553000000.0000
Solution quality estimate total_estimate	0.6361
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	58.0 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.256
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	155100000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 0.006; Positv: 1.000; Valcen: 0.968; Smooth: 0.952

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase subunit e 1
Molecular weight formula_weight	9380.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e
Atom count atom_count	50652

MAYHGLTVPLIVMSVFWGFVGFLVPWFIPKGPNRGVIITMLVTCSVCCYLFWLIAILAQLNPLFGPQLKNETIWYLKYHWP

Entity 2 Entity 2 polymer

Description description	Ribonuclease kappa
Molecular weight formula_weight	15435.2 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f

MGWLRPGPRPLCPPARASWAFSHRFPSPLAPRRSPTPFFMASLLCCGPKLAACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNLYEQVSYNCFIAAGLYLLLGGFSFCQVRLNKRKEYMVR

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit S1
Molecular weight formula_weight	52067.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	o

MMAAMATARVRMGPRCAQALWRMPWLPVFLSLAAAAAAAAAEQQVPLVLWSSDRDLWAPAADTHEGHITSDLQLSTYLDPALELGPRNVLLFLQDKLSIEDFTAYGGVFGNKQDSAFSNLENALDLAPSSLVLPAVDWYAVSTLTTYLQEKLGASPLHVDLATLRELKLNASLPALLLIRLPYTASSGLMAPREVLTGNDEVIGQVLSTLKSEDVPYTAALTAVRPSRVARDVAVVAGGLGRQLLQKQPVSPVIHPPVSYNDTAPRILFWAQNFSVAYKDQWEDLTPLTFGVQELNLTGSFWNDSFARLSLTYERLFGTTVTFKFILANRLYPVSARHWFTMERLEVHSNGSVAYFNASQVTGPSIYSFHCEYVSSLSKKGSLLVARTQPSPWQMMLQDFQIQAFNVMGEQFSYASDCASFFSPGIWMGLLTSLFMLFIFTYGLHMILSLKTMDRFDDHKGPTISLTQIV

Entity 4 Entity 4 polymer

Description description	Renin receptor
Molecular weight formula_weight	39045.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

MAVFVVLLALVAGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATVMVMVKGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTLRQLRNRLFQENSVLSSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDEIGKRYGEDSEQFRDASKILVDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRTILEAKQAKNPASPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRMD

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase 21 kDa proteolipid subunit
Molecular weight formula_weight	21418.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

MTGLALLYSGVFVAFWACALAVGVCYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGGVKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATDPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMGD

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase 16 kDa proteolipid subunit
Molecular weight formula_weight	15743.7 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,g,h,i,j,k,l,m,n

MSESKSGPEYASFFAVMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEQIMKSIIPVVMAGIIAIYGLVVAVLIANSLNDDISLYKSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK

Entity 7 Entity 7 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 8 Entity 8 polymer

Description description	V-type proton ATPase 116 kDa subunit a 4
Molecular weight formula_weight	99168.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MVSVFRSEEMCLSQLFLQVEAAYCCVAELGELGLVQFKDLNMNVNSFQRKFVNEVRRCESLERILRFLEDEMQNEIVVQLLEKSPLTPLPREMITLETVLEKLEGELQEANQNQQALKQSFLELTELKYLLKKTQDFFETETNLADDFFTEDTSGLLELKAVPAYMTGKLGFIAGVINRERMASFERLLWRICRGNVYLKFSEMDAPLEDPVTKEEIQKNIFIIFYQGEQLRQKIKKICDGFRATVYPCPEPAVERREMLESVNVRLEDLITVITQTESHRQRLLQEAAANWHSWLIKVQKMKAVYHILNMCNIDVTQQCVIAEIWFPVADATRIKRALEQGMELSGSSMAPIMTTVQSKTAPPTFNRTNKFTAGFQNIVDAYGVGSYREINPAPYTIITFPFLFAVMFGDCGHGTVMLLAALWMILNERRLLSQKTDNEIWNTFFHGRYLILLMGIFSIYTGLIYNDCFSKSLNIFGSSWSVQPMFRNGTWNTHVMEESLYLQLDPAIPGVYFGNPYPFGIDPIWNLASNKLTFLNSYKMKMSVILGIVQMVFGVILSLFNHIYFRRTLNIILQFIPEMIFILCLFGYLVFMIIFKWCCFDVHVSQHAPSILIHFINMFLFNYSDSSNAPLYKHQQEVQSFFVVMALISVPWMLLIKPFILRASHRKSQLQASRIQEDATENIEGDSSSPSSRSGQRTSADTHGALDDHGEEFNFGDVFVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVMNSGLQTRGWGGIVGVFIIFAVFAVLTVAILLIMEGLSAFLHALRLHWVEFQNKFYVGDGYKFSPFSFKHILDGTAEEGDLDYKDDDDKLDYKDDDDKADL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 9 Entity 9 polymer

Description description	Anti V-ATPase Nanobody 2CAS66
Molecular weight formula_weight	15142.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	q

MGQVQLQESGGGLVQAGGSLRLSCAGSGRTFTYHTMGWFRQAPGKEREFVASINWSDTRLYYTDSVKGRFTISRDNAKSTVYLQMNSLKPEDTAVYYCVATAMTTGATMTVDNVDYWGQGTQVTVSSAAALEVLFQGPK

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 10 Entity 10 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	8

Entity 11 Entity 11 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 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	3

Entity 13 Entity 13 non-polymer

Description description	Cladoniamide A
Molecular weight formula_weight	437.8 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 14 Entity 14 non-polymer

Description description	methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate
Molecular weight formula_weight	534.6 kDa
Source method src_method	syn
Copy count entity_count	1

▶

8. Citations (1)

▶

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	—

Resolution resolution	3.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	144439

fit	/app/data/saxs_computation/de/9det/9det.fit
pddf	/app/data/pr_computation/de/9det/9det.pr.out
profile	/app/data/saxs_computation/de/9det/9det.dat

Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor

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

V-type proton ATPase subunit e 1

State in the Current Structure

Other States of the Same Protein in the Database

Ribonuclease kappa

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

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 16 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 116 kDa subunit a 4

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 (14)

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

来源 Source

Entity 9 Entity 9 polymer

Polymer Polymer

来源 Source

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)