8xli

Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus

Method: ELECTRON MICROSCOPY D_max: 143.2 Å Quality: GOOD

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

V-type proton ATPase 116 kDa subunit a 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	Other combination Heteromer Protein × 16 其他Polymer 4 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain a； UniProt 4–831	Not recorded	ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 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 8XLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
6VQI Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å
6VQJ Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
6VQK Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 5.70 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain a 1–838（838 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain a 1–826（826 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B8Q Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Deposited 2024-03-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain a 1–838（838 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric	Chain a 1–832（832 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPP1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain a； PDBConstruct 1–828； UniProt 4–831

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

OrganismNot specified

UniProt B0K022

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 16 其他Polymer 4 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain b； UniProt 2–204	Not recorded	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8XLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain b 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain b 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain b 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain b 1–205（205 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain b 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain b 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric	Chain b 1–205（205 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B0K022_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain b； PDBConstruct 1–203； UniProt 2–204

V-type proton ATPase subunit S1

OrganismNot specified

UniProt O54715

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 16 其他Polymer 4 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain c； UniProt 248–451	Not recorded	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8XLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain c 1–463（463 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain c 1–463（463 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain c 1–463（463 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain c 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain P 1–463（463 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain P 1–463（463 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain P 1–463（463 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric	Chain P 1–463（463 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAS1_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain c； PDBConstruct 1–204； UniProt 248–451

V-type proton ATPase subunit e 2

OrganismNot specified

UniProt Q5EB76

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 16 其他Polymer 4 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain e； UniProt 3–79	Not recorded	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8XLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain e 1–81（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain e 1–81（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain e 1–81（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain e 1–81（81 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain e 1–81（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain e 1–81（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric	Chain e 1–81（81 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VA0E2_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain e； PDBConstruct 1–77； UniProt 3–79

V-type proton ATPase 16 kDa proteolipid subunit c

OrganismNot specified

UniProt P63081

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 16 其他Polymer 4 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain g； UniProt 6–155 Chain h； UniProt 6–155 Chain i； UniProt 6–155 Chain j； UniProt 6–155 Chain k； UniProt 6–155 Chain l； UniProt 6–155 Chain m； UniProt 6–155 Chain n； UniProt 6–155 Chain o； UniProt 6–155	Not recorded	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8XLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric	Chain g 1–155（155 aa） Chain h 1–155（155 aa） Chain i 1–155（155 aa） Chain j 1–155（155 aa） Chain k 1–155（155 aa） Chain l 1–155（155 aa） Chain m 1–155（155 aa） Chain n 1–155（155 aa） Chain o 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VATL_RAT
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain g； PDBConstruct 1–150； UniProt 6–155 Author chain h； PDBConstruct 1–150； UniProt 6–155 Author chain i； PDBConstruct 1–150； UniProt 6–155 Author chain j； PDBConstruct 1–150； UniProt 6–155 Author chain k； PDBConstruct 1–150； UniProt 6–155 Author chain l； PDBConstruct 1–150； UniProt 6–155 Author chain m； PDBConstruct 1–150； UniProt 6–155 Author chain n； PDBConstruct 1–150； UniProt 6–155 Author chain o； PDBConstruct 1–150； UniProt 6–155

Renin receptor cytoplasmic fragment

OrganismNot specified

UniProt Q6AXS4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 16 其他Polymer 4 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain p； UniProt 292–340	Not recorded	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8XLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VQ6 Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQ7 Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å
6VQ8 Mammalian V-ATPase from rat brain - composite model of rotational state 3 bound to ADP and SidK (built from focused refinement models) Deposited 2020-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
6VQC Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement) Deposited 2020-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain p 1–350（350 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
6VQG Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 2 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain p 1–350（350 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
6VQH Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 3 (from focused refinement) Deposited 2020-02-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain p 1–350（350 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
7UZF Rat Kidney V-ATPase with SidK, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZG Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 1 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7UZH Rat Kidney V-ATPase with SidK, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7UZI Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 Deposited 2022-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9B8O Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo Deposited 2024-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain p 1–350（350 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 PTY PHOSPHATIDYLETHANOLAMINE × 9 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9BRB Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain p 1–350（350 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BRC Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 Deposited 2024-05-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain p 1–350（350 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9BRD Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 Deposited 2024-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 36 PDB declaration: 36-meric	Chain p 1–350（350 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PTY PHOSPHATIDYLETHANOLAMINE × 9 WJP methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LP3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 CLR CHOLESTEROL × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RENR_RAT
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain p； PDBConstruct 1–49； UniProt 292–340

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8xli
Deposition date deposition_date	2023-12-26
Structure title title	Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus
Keywords keywords	Vo sector of V-ATPase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	45.47 Å
Radius of gyration Rg (electron density) rg_electron	44.52 Å
Forward intensity I(0) i0	1338270000.00
Molecular weight molecular_weight	327060.0 kDa
Excluded volume excluded_volume	418920 Å³
Envelope volume envelope_volume	584320 Å³
Hydration-shell volume shell_volume	103310 Å³
Envelope diameter envelope_diameter	152.4 Å
Shell Rg shell_rg	53.80 Å
Envelope Rg envelope_rg	43.78 Å
Shape Rg shape_rg	44.54 Å
Total Rg total_rg	44.83 Å
Total atoms total_atoms	23024
Residues n_residues	3075
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	143.2 Å
Rg (real space) rg_real	45.18 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	1.3380e+09
I(0) uncertainty (real space) i0_real_error	2.4150e+07
Rg (reciprocal space) rg_reciprocal	45.46 Å
I(0) (reciprocal space) i0_reciprocal	1339000000.0000
Solution quality estimate total_estimate	0.8804
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	57.3 Å
Skewness Skewness skewness	0.156
Kurtosis Kurtosis kurtosis	-0.376
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	143000000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.872

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase 116 kDa subunit a 1
Molecular weight formula_weight	95248.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a
Atom count atom_count	23024

LFRSEEMTLAQLFLQSEAAYCCVSELEELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLEESSSLLEPNEMGRGAPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTHGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGLIYNDCFSKSLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIHFINMFLFSYPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQYLRKKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDAEEPTEDEVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYTGTGFKFLPFSFEHI

Entity 2 Entity 2 polymer

Description description	ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
Molecular weight formula_weight	21372.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

TGLELLYLGIFVAFWACMIVVGICYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGGVKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATDPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMG

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit S1
Molecular weight formula_weight	23360.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c

IHPPVSYNDTAPRILFWAQNFSVAYKDEWKDLTSLTFGVENLNLTGSFWNDSFAMLSLTYEPLFGATVTFKFILASRFYPVSARYWFTMERLEIHSNGSVAHFNVSQVTGPSIYSFHCEYVSSLSKKGSLLVTNVPSLWQMTLHNFQIQAFNVTGEQFSYASDCAGFFSPGIWMGLLTTLFMLFIFTYGLHMILSLKTMDRFDD

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit
Molecular weight formula_weight	39285.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

SFFPELYFNVDNGYLEGLVRGLKAGVLSQADYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVIDDKLKEKMVVEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQKCHPLGSFEQMEAVNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDAMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCPILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGRLYPEGLAQLARADDYEQVKNVADYYPEYKLLFEGAGSNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVKLKEQECRNIVWIAECIAQRHRAKIDNYIPIF

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit e 2
Molecular weight formula_weight	8655.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e

AHSFALPVIIFTTFWGLIGIAGPWFVPKGPNRGVIITMLVATAVCCYLFWLIAILAQLNPLFGPQLKNETIWYVRFL

Entity 6 Entity 6 polymer

Description description	Ribonuclease K
Molecular weight formula_weight	9933.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f

CCGPKLAACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNLYEQVSYNCFIAAGLYLLLGGFSFCQVRLNKRKE

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase 16 kDa proteolipid subunit c
Molecular weight formula_weight	15256.1 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

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

NNPEYSSFFGVMGASSAMVFSAMGAAYGTAKSGTGIAAMSVMRPELIMKSIIPVVMAGIIAIYGLVVAVLIANSLTDGITLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK

Entity 8 Entity 8 polymer

Description description	Renin receptor cytoplasmic fragment
Molecular weight formula_weight	5740.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

PYNLAYKYNLEYSVVFNLVLWIMTGLALAVIITSYNIWNMDPGYDSIIY

Entity 9 Entity 9 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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

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

Resolution resolution	3.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	34147

fit	/app/data/saxs_computation/xl/8xli/8xli.fit
pddf	/app/data/pr_computation/xl/8xli/8xli.pr.out
profile	/app/data/saxs_computation/xl/8xli/8xli.dat

Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus

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

V-type proton ATPase 116 kDa subunit a 1

State in the Current Structure

Other States of the Same Protein in the Database

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

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

V-type proton ATPase subunit e 2

State in the Current Structure

Other States of the Same Protein in the Database

V-type proton ATPase 16 kDa proteolipid subunit c

State in the Current Structure

Other States of the Same Protein in the Database

Renin receptor cytoplasmic fragment

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 (9)

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 branched

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)