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)
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8qby
Q-score: 0.683
Ivanov BS, Bridges HR, Hirst J, Jarman OD
To Be Published
- Respiratory complex i (Complex from Paracoccus denitrificans PD1222)
- Nadh-quinone oxidoreductase subunit n (52 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh dehydrogenase subunit m (56 kDa, Protein from Paracoccus denitrificans PD1222)
- Etc complex i subunit conserved region (12 kDa, Protein from Paracoccus denitrificans PD1222)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Nadh-quinone oxidoreductase chain 10 (21 kDa, Protein from Paracoccus denitrificans PD1222)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Nadh-quinone oxidoreductase (73 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh dehydrogenase subunit l (77 kDa, Protein from Paracoccus denitrificans PD1222)
- Water (18 Da, Ligand)
- Nadh-quinone oxidoreductase subunit h (38 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh-quinone oxidoreductase subunit d (46 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh-quinone oxidoreductase subunit i (18 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh:ubiquinone oxidoreductase 17.2 kd subunit (14 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Paracoccus denitrificans PD1222)
- Ubiquinone-10 (863 Da, Ligand)
- Nadh-quinone oxidoreductase subunit c (23 kDa, Protein from Paracoccus denitrificans PD1222)
- Zinc ion (65 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Protein-l-isoaspartate o-methyltransferase (23 kDa, Protein from Paracoccus denitrificans PD1222)
- Sodium ion (22 Da, Ligand)
- Zinc finger chcc-type domain-containing protein (7 kDa, Protein from Paracoccus denitrificans PD1222)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Paracoccus denitrificans PD1222)
- Iron/sulfur cluster (351 Da, Ligand)
- Nadh-quinone oxidoreductase subunit b (19 kDa, Protein from Paracoccus denitrificans PD1222)
- Cardiolipin (1 kDa, Ligand)
- Nadh dehydrogenase subunit e (26 kDa, Protein from Paracoccus denitrificans PD1222)
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 l (11 kDa, Protein from Thermococcus kodakarensis)
- 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)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (13 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 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 l (11 kDa, Protein from Thermococcus kodakarensis)
- 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)
- Ftta-dependent transcription termination complex containing 52 nt rna (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Rna (29-mer) (16 kDa, RNA from synthetic construct)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9b8p
Q-score: 0.529
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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- V-type proton atpase subunit g (13 kDa, Protein from Rattus norvegicus)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit b, brain isoform (56 kDa, Protein from Rattus norvegicus)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, v1 (Complex from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
- Sidk (65 kDa, Protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1)
- H(+)-transporting two-sector atpase (71 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit e 1 (26 kDa, Protein from Rattus norvegicus)
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 ]
- V-type proton atpase 116 kda subunit a 1 (94 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit s1 (51 kDa, Protein from Rattus norvegicus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Atpase h+-transporting v1 subunit d (28 kDa, Protein from Rattus norvegicus)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- V-type proton atpase subunit e 2 (9 kDa, Protein from Rattus norvegicus)
- Synaptic vesicle v-atpase with synaptophysin and sidk, state 3, vo (Complex from Rattus norvegicus)
- Phosphatidylethanolamine (734 Da, Ligand)
- Synaptophysin (33 kDa, Protein from Rattus norvegicus)
- Renin receptor (39 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit (40 kDa, Protein from Rattus norvegicus)
- Rnasek protein (9 kDa, Protein from Rattus norvegicus)
- V-type proton atpase subunit f (13 kDa, Protein from Rattus norvegicus)
- Methyl (3r,6z,10e,14e)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate (534 Da, Ligand)
- (7r)-4,7-dihydroxy-n,n,n-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide (524 Da, Ligand)
- V-type proton atpase 16 kda proteolipid subunit c (15 kDa, Protein from Rattus norvegicus)
- Cholesterol (386 Da, Ligand)
- Atpase, h+ transporting, v0 subunit b (predicted), isoform cra_a (21 kDa, Protein from Rattus norvegicus)
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 f, mitochondrial (10 kDa, Protein from Homo sapiens)
- Human atp synthase (Complex from Homo sapiens)
- Atp synthase subunit g, mitochondrial (11 kDa, Protein from Homo sapiens)
- Atp synthase subunit gamma, mitochondrial (30 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp synthase subunit alpha, mitochondrial (55 kDa, Protein from Homo sapiens)
- Atp synthase subunit beta, mitochondrial (51 kDa, Protein from Homo sapiens)
- Atp synthase subunit d, mitochondrial (18 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Atp synthase subunit o, mitochondrial (20 kDa, Protein from Homo sapiens)
- Atp synthase subunit atp5mj, mitochondrial (6 kDa, Protein from Homo sapiens)
- Atpase inhibitor, mitochondrial (9 kDa, Protein from Homo sapiens)
- Bedaquiline (555 Da, Ligand)
- Atp synthase f(0) complex subunit c1, mitochondrial (7 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Atp synthase f(0) complex subunit b1, mitochondrial (24 kDa, Protein from Homo sapiens)
- Atp synthase subunit delta, mitochondrial (15 kDa, Protein from Homo sapiens)
- Atp synthase subunit e, mitochondrial (7 kDa, Protein from Homo sapiens)
- Atp synthase-coupling factor 6, mitochondrial (12 kDa, Protein from Homo sapiens)
- Atp synthase subunit epsilon, mitochondrial (5 kDa, Protein from Homo sapiens)
- Atp synthase protein 8 (8 kDa, Protein from Homo sapiens)
- Atp synthase subunit a (24 kDa, Protein from Homo sapiens)
human co-transcriptional RNA capping enzyme RNGTT
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w8e
Q-score: 0.265
Nat Commun (2024) 15 pp. 4622-4622 [ Pubmed: 38816438 DOI: doi:10.1038/s41467-024-48963-1 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Human co-transcriptional rna capping enzyme rngtt (Complex)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor, transcription elongation factor, mrna-capping enzyme (Complex from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polimerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Dna,rna (Complex from Homo sapiens)
- Rna (5'-d(*(gtp))-r(p*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
human co-transcriptional RNA capping enzyme RNGTT-CMTR1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8w8f
Q-score: 0.228
Nat Commun (2024) 15 pp. 4622-4622 [ Pubmed: 38816438 DOI: doi:10.1038/s41467-024-48963-1 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Human co-transcriptional rna capping enzyme rngtt-cmtr1 (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*gp*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Dna-rna (Complex from Homo sapiens)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Transcription elongation factor, m-rna capping enzyme, cmtr1 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
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)