Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9b8o
Q-score: 0.513
Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL
Science (2024) 385 pp. 168-174 [ DOI: doi:10.1126/science.adp5577 Pubmed: 38900912 ]
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Methyl (3r,6z,10e,14e)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate (534 Da, Ligand)
- Renin receptor (39 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Rattus norvegicus)
- (7r)-4,7-dihydroxy-n,n,n-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide (524 Da, Ligand)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, vo (Complex from Rattus norvegicus)
- V-type proton atpase 116 kda subunit a 1 (94 kDa, Protein from Rattus norvegicus)
- Phosphatidylethanolamine (734 Da, Ligand)
- Synaptophysin (33 kDa, Protein from Rattus norvegicus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Rattus norvegicus)
- Cholesterol (386 Da, Ligand)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Rnasek protein (9 kDa, Protein from Rattus norvegicus)
- Atpase, h+ transporting, v0 subunit b (predicted), isoform cra_a (21 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit (40 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
Intact V-ATPase State 2 and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9bra
Q-score: 0.284
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
Intact V-ATPase State 3 and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9brq
Q-score: 0.271
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
Intact V-ATPase State 3 in synaptophysin knock-out isolated synaptic vesicles
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 9brr
Q-score: 0.3
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9brs
Q-score: 0.277
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
Intact V-ATPase State 1 and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9brt
Q-score: 0.271
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
Intact V-ATPase State 1 in synaptophysin knock-out isolated synaptic vesicles
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9bru
Q-score: 0.262
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9bry
Q-score: 0.373
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (32 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- Beta-d-mannopyranose (180 Da, Ligand)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9brz
Q-score: 0.385
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024) 631 pp. 899-904 [ DOI: doi:10.1038/s41586-024-07610-x Pubmed: 38838737 ]
- V-type proton atpase 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)