Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9e76
Q-score: 0.507
Knight K, Park JB, Oot RA, Khan MM, Roh SH, Wilkens S
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.10.632502 Pubmed: 39829782 ]
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase subunit f (9 kDa, Protein from Saccharomyces cerevisiae)
- Nanobody 1wva25 (16 kDa, Protein from Lama glama)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase vo proton channel subcomplex bound to nanobody 1wva25 (400 kDa, Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 9e7l
Q-score: 0.514
Knight K, Park JB, Oot RA, Khan MM, Roh SH, Wilkens S
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.10.632502 Pubmed: 39829782 ]
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase subunit f (9 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase vo proton channel bound to nanobody 2wva7 (540 kDa, Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae)
- Nanobody 2wva7 (14 kDa, Protein from Lama glama)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
Yeast V-ATPase Vo proton channel bound to nanobody 2WVA149
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 9mj4
Q-score: 0.455
Knight K, Park JB, Oot RA, Khan MM, Roh SH, Wilkens S
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.10.632502 Pubmed: 39829782 ]
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase subunit f (9 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase vo proton channel subcomplex bound to nanobody 2wva149 (400 kDa, Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae)
- Nanobody 2wva149 (15 kDa, Protein from Lama glama)
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
Yeast RAVE bound to V-ATPase V1 complex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9cop
Q-score: 0.252
Wang H, Tarsio M, Kane PM, Rubinstein JL
PNAS (2024) 121 pp. e2414511121-e2414511121 [ Pubmed: 39625975 DOI: doi:10.1073/pnas.2414511121 ]
- V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae)
- Regulator of v-atpase in vacuolar membrane protein 2 (40 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Suppressor of kinetochore protein 1 (22 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rave bound to v-atpase v1 complex (Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit g (12 kDa, Protein from Saccharomyces cerevisiae)
- Regulator of v-atpase in vacuolar membrane protein 1 (155 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- V-type proton atpase subunit h (54 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase catalytic subunit a (118 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae)
Yeast ATP synthase map in conformation-1 at pH 6
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8f29
Q-score: 0.301
Sharma S, Luo M, Patel H, Mueller DM, Liao M
Nat Struct Mol Biol (2024) 31 pp. 657-666 [ Pubmed: 38316880 DOI: doi:10.1038/s41594-024-01219-4 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit d, mitochondrial (19 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase protein 8 (5 kDa, Protein from Saccharomyces cerevisiae)
- Phosphate ion (94 Da, Ligand)
- Atp synthase subunit j, mitochondrial (4 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit epsilon, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit h, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit beta, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit f, mitochondrial (9 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit a (25 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 9, mitochondrial (7 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit alpha, mitochondrial (54 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit delta, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 5, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 4, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit gamma, mitochondrial (28 kDa, Protein from Saccharomyces cerevisiae)
Yeast ATP synthase map in conformation-2, at pH 6
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8f39
Q-score: 0.301
Sharma S, Luo M, Patel H, Mueller DM, Liao M
Nat Struct Mol Biol (2024) 31 pp. 657-666 [ Pubmed: 38316880 DOI: doi:10.1038/s41594-024-01219-4 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit d, mitochondrial (19 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase protein 8 (5 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit j, mitochondrial (4 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit epsilon, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit h, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit beta, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit f, mitochondrial (9 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit gamma, mitochondrial (29 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 4, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 5, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 9, mitochondrial (7 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit alpha, mitochondrial (54 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit delta, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit a (25 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Atp synthase (Complex from Saccharomyces cerevisiae)
Yeast ATP Synthase in conformation-3, at pH 6
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8fkj
Q-score: 0.321
Sharma S, Luo M, Patel H, Mueller DM, Liao M
Nat Struct Mol Biol (2024) 31 pp. 657-666 [ Pubmed: 38316880 DOI: doi:10.1038/s41594-024-01219-4 ]
- Atp synthase subunit d, mitochondrial (19 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase protein 8 (5 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit epsilon, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 9, mitochondrial (7 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit beta (50 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit h, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit f, mitochondrial (9 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase (Complex from Saccharomyces cerevisiae)
- Atp synthase subunit 5, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 4, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit gamma (29 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit a (25 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit delta, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Atp18 isoform 1 (4 kDa, Protein from Saccharomyces cerevisiae)
Yeast ATP Synthase map in presence of MgATP
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8fl8
Q-score: 0.285
Sharma S, Luo M, Patel H, Mueller DM, Liao M
Nat Struct Mol Biol (2024) 31 pp. 657-666 [ Pubmed: 38316880 DOI: doi:10.1038/s41594-024-01219-4 ]
- Atp synthase subunit gamma, mitochondrial (29 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase protein 8 (5 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit d, mitochondrial (19 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit epsilon, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit beta (50 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit h, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit f, mitochondrial (9 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase (Complex from Saccharomyces cerevisiae)
- Atp synthase subunit 5, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 4, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit 9, mitochondrial (7 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp synthase subunit delta, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Atp synthase subunit a (25 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Atp18 isoform 1 (4 kDa, Protein from Saccharomyces cerevisiae)
Yeast VO in complex with Vma12-22p
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8eas
Q-score: 0.606
Wang H, Bueler SA, Rubinstein JL
PNAS (2023) 120 pp. e2217181120-e2217181120 [ Pubmed: 36724250 DOI: doi:10.1073/pnas.2217181120 ]
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase assembly factor vma12p (16 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- Yeast v-atpase subunit f (9 kDa, Protein from Saccharomyces cerevisiae)
- Yeast vo in complex with vma12-22p (Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit a, vacuolar isoform (95 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae)
- Vacuolar atpase assembly protein vma22 (21 kDa, Protein from Saccharomyces cerevisiae)
Yeast VO missing subunits a, e, and f in complex with Vma12-22p
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8eat
Q-score: 0.529
Wang H, Bueler SA, Rubinstein JL
PNAS (2023) 120 pp. e2217181120-e2217181120 [ Pubmed: 36724250 DOI: doi:10.1073/pnas.2217181120 ]
- V-type proton atpase subunit c'' (22 kDa, Protein from Saccharomyces cerevisiae)
- V0 assembly protein 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c' (17 kDa, Protein from Saccharomyces cerevisiae)
- Vacuolar atpase assembly protein vma22 (21 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae)
- Yeast vo missing subunits a, e, and f in complex with vma12-22p (Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae)
- Vacuolar atpase assembly integral membrane protein vph2 (25 kDa, Protein from Saccharomyces cerevisiae)