Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9bct
Q-score: 0.554
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Rna (13 kDa, RNA from synthetic construct)
- Ftta-dependent transcription termination complex (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9bcu
Q-score: 0.613
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Rna (29-mer) (16 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex containing 52 nt rna (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
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 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 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 d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component 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 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 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 d 1 (40 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 s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component 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 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 21 kda proteolipid subunit c'' (21 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 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 d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component 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 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 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 h (55 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 21 kda proteolipid subunit c'' (21 kDa, Protein from Mus musculus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 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)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component 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 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Mus musculus)
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit h (55 kDa, Protein from Mus musculus)
- V-type proton atpase 116 kda subunit a 1 (96 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 d 1 (40 kDa, Protein from Mus musculus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 kDa, Protein from Mus musculus)
- V-type proton atpase catalytic subunit a (68 kDa, Protein from Mus musculus)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Mus musculus)
- Synaptophysin (34 kDa, Protein from Mus musculus)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- Mouse brain isolated glutamatergic synaptic vesicles (Cellular component 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 [ Pubmed: 38838737 DOI: doi:10.1038/s41586-024-07610-x ]
- V-type proton atpase subunit g 2 (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 1 (26 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 h (55 kDa, Protein from Mus musculus)
- V-type proton atpase subunit e 2 (9 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 s1 (51 kDa, Protein from Mus musculus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d (28 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)
- Renin receptor cytoplasmic fragment (39 kDa, Protein from Mus musculus)
- Ribonuclease kappa (11 kDa, Protein from Mus musculus)
- V-type proton atpase subunit f (13 kDa, Protein from Mus musculus)
- V-type proton atpase subunit c 1 (43 kDa, Protein from Mus musculus)
- V-type proton atpase subunit d 1 (40 kDa, Protein from Mus musculus)
- Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles (Cellular component from Mus musculus)
Structure of the human ATP synthase bound to bedaquiline (membrane domain)
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8khf
Q-score: 0.508
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ Pubmed: 38961288 DOI: doi:10.1038/s41586-024-07605-8 ]
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Atp synthase subunit f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
Structure of the human ATP synthase bound to bedaquiline (composite)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8ki3
Q-score: 0.547
Zhang Y, Lai Y, Zhou S, Ran T, Zhang Y, Zhao Z, Feng Z, Yu L, Xu J, Shi K, Wang J, Pang Y, Li L, Chen H, Guddat LW, Gao Y, Liu F, Rao Z, Gong H
Nature (2024) 631 pp. 409-414 [ Pubmed: 38961288 DOI: doi:10.1038/s41586-024-07605-8 ]
- Atp synthase subunit alpha, mitochondrial (55 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
- Atp synthase subunit o, mitochondrial (20 kDa, Protein from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp synthase subunit f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Atp synthase subunit beta, mitochondrial (51 kDa, Protein from Homo sapiens)
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atpase inhibitor, mitochondrial (9 kDa, Protein from Homo sapiens)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
- Atp synthase-coupling factor 6, mitochondrial (12 kDa, Protein from Homo sapiens)