Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9jm0
Q-score: 0.492
Wang Y, Wang C, Guan Z, Cao J, Xu J, Wang S, Cui Y, Wang Q, Chen Y, Yin Y, Zhang D, Liu H, Sun M, Jin S, Tao P, Zou T
Cell Rep (2024) 43 pp. 114857-114857 [ DOI: doi:10.1016/j.celrep.2024.114857 Pubmed: 39395169 ]
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Retron ec86 reverse transcriptase (37 kDa, Protein from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Rna (82-mer) (26 kDa, RNA from Escherichia coli)
- Retron ec86 putative ribosyltransferase/dna-binding protein (35 kDa, Protein from Escherichia coli)
- Nicotinamide (122 Da, Ligand)
- Retron ec86-effector fiber (Complex from Escherichia coli)
- Rna (5'-r(p*cp*gp*up*ap*ap*gp*gp*gp*up*gp*cp*gp*cp*a)-3') (4 kDa, RNA from Escherichia coli)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7mca
Q-score: 0.441
Feng X, Noguchi Y, Barbon M, Stillman B, Speck C, Li H
Nat Commun (2021) 12 pp. 3883-3883 [ Pubmed: 34162887 DOI: doi:10.1038/s41467-021-24199-1 ]
- Magnesium ion (24 Da, Ligand)
- Complex of origin replication complex with cdc6 and ars1 origin dna (470 kDa, Complex from Saccharomyces cerevisiae)
- Dna (85-mer) (26 kDa, DNA from Saccharomyces cerevisiae)
- Origin recognition complex subunit 5 (55 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Dna (85-mer) (26 kDa, DNA from Saccharomyces cerevisiae)
- Origin recognition complex subunit 6 (50 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 1 (104 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 6 (58 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 4 (60 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Origin recognition complex subunit 2 (71 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM 3D map of the S. cerevisiae origin recognition complex bound to Cdc6 and ARS1 origin DNA
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7mca
Q-score: -0.014
Feng X, Noguchi Y, Barbon M, Stillman B, Speck C, Li H
Nat Commun (2021) 12 pp. 3883-3883 [ DOI: doi:10.1038/s41467-021-24199-1 Pubmed: 34162887 ]
- Origin recognition complex subunit 1 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 3 (Protein from Saccharomyces cerevisiae)
- Ars1 dna(85-mer) (DNA from Saccharomyces cerevisiae)
- Origin recognition complex subunit 6 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 5 (Protein from Saccharomyces cerevisiae)
- Cell division control protein 6 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 4 (Protein from Saccharomyces cerevisiae)
- Complex of origin replication complex with cdc6 and ars1 origin dna (470 kDa, Complex from Saccharomyces cerevisiae)
- Origin recognition complex subunit 2 (Protein from Saccharomyces cerevisiae)
TFIID-based core PIC on PUMA promoter
Resolution: 7.4 Å
EM Method: Single-particle
Fitted PDBs: 7eg8
Q-score: 0.074
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Tfiif (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- Tfiia (Complex from Homo sapiens)
- Dna(scp promoters) (Complex)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Tfiid-based core pic on puma promoter (Complex)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
TFIID-based intermediate PIC on PUMA promoter
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7ega
Q-score: 0.122
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Tfiib (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (167 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Dna(puma promoters) (Complex)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- Tfiid-based intermediate pic on puma promoter (Complex)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6psq
Q-score: 0.479
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpc (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6psr
Q-score: 0.48
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Chapso (631 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpi1 (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6pss
Q-score: 0.446
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and mutant rpst p2 as trpi1.5a (Complex from Escherichia coli)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6pst
Q-score: 0.514
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Chapso (631 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and mutant rpst p2 as trpi1.5b (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6psu
Q-score: 0.426
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell (2020) 78 pp. 275- [ Pubmed: 32160514 DOI: doi:10.1016/j.molcel.2020.02.017 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpi2 (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)