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 [ DOI: doi:10.1038/s41467-021-24199-1 Pubmed: 34162887 ]
- Cell division control protein 6 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna (85-mer) (26 kDa, DNA from Saccharomyces cerevisiae)
- Origin recognition complex subunit 2 (71 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 5 (55 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Origin recognition complex subunit 6 (50 kDa, Protein from Saccharomyces cerevisiae)
- Dna (85-mer) (26 kDa, DNA from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Origin recognition complex subunit 4 (60 kDa, 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 1 (104 kDa, Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 3 (72 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 ]
- Ars1 dna(85-mer) (DNA from Saccharomyces cerevisiae)
- Cell division control protein 6 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 1 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 2 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 4 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 6 (Protein from Saccharomyces cerevisiae)
- Origin recognition complex subunit 5 (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 3 (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 ]
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- 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)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Tfiid-based core pic on puma promoter (Complex)
- Zinc ion (65 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Dna(scp promoters) (Complex)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
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 iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- 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)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (167 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna(puma promoters) (Complex)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Tfiid-based intermediate pic on puma promoter (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Tfiib (Complex from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Dna (85-mer) (26 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
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- [ DOI: doi:10.1016/j.molcel.2020.02.017 Pubmed: 32160514 ]
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpc (Complex from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 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- [ DOI: doi:10.1016/j.molcel.2020.02.017 Pubmed: 32160514 ]
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- 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 trpi1 (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 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- [ DOI: doi:10.1016/j.molcel.2020.02.017 Pubmed: 32160514 ]
- 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 trpi1.5a (Complex from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 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)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein 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- [ DOI: doi:10.1016/j.molcel.2020.02.017 Pubmed: 32160514 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Escherichia coli sigma70-holoenzyme bound to trar and mutant rpst p2 as trpi1.5b (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)
- 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)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
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- [ DOI: doi:10.1016/j.molcel.2020.02.017 Pubmed: 32160514 ]
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as trpi2 (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6psv
Q-score: 0.468
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- [ DOI: doi:10.1016/j.molcel.2020.02.017 Pubmed: 32160514 ]
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Escherichia coli sigma70-holoenzyme bound to trar and wildtype rpst p2 as tprerpo (Complex from Escherichia coli)
- Protein trar (8 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)