E.coli RNAP-RapA elongation complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7m8e
Q-score: 0.455
Shi W, Zhou W, Chen M, Yang Y, Hu Y, Liu B
Nucleic Acids Res (2021) 49 pp. 10707-10716 [ Pubmed: 34428297 DOI: doi:10.1093/nar/gkab744 ]
- Rna polymerase-associated protein rapa (110 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (39-mer) (12 kDa, DNA from Escherichia coli)
- Rnap-rapa elongation complex (530 kDa, Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*ap*up*cp*gp*gp*cp*up*cp*a)-3') (2 kDa, RNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Nontemplate dna (39-mer) (11 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6xl5
Q-score: 0.541
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Water (18 Da, Ligand)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Ecmrr-rnap-promoter open complex (ecmrr-rpo) (Complex from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6xl9
Q-score: 0.517
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Water (18 Da, Ligand)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Ecmrr-rnap-promoter initial transcribing complex with 3-nt rna transcript (ecmrr-rpitc-3nt) (Complex from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Rna (5'-d(*(gtp))-r(p*ap*g)-3') (1 kDa, RNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6xlj
Q-score: 0.512
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Rna (5'-d(*(gtp))-r(p*cp*ap*g)-3') (1 kDa, RNA from Escherichia coli O157:H7)
- Ecmrr-rnap-promoter initial transcribing complex with 4-nt rna transcript (ecmrr-rpitc-4nt) (Complex from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6xll
Q-score: 0.519
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Rnap-promoter initial transcribing complex with 5-nt rna transcript (rpitc-5nt) (Complex from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Rna transcript (5-mer) (1 kDa, RNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6xlm
Q-score: 0.462
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ Pubmed: 33976201 DOI: doi:10.1038/s41467-021-22990-8 ]
- 9-nt rna transcript (2 kDa, RNA from Escherichia coli O157:H7)
- E. coli rnap-dna elongation complex 1 (rde1) (Complex from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 6xln
Q-score: 0.528
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun (2021) 12 pp. 2702-2702 [ DOI: doi:10.1038/s41467-021-22990-8 Pubmed: 33976201 ]
- Chapso (631 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- E. coli rnap-dna elongation complex 2 (rde2) (Complex from Escherichia coli O157:H7)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)
- 9-nt rna transcript (2 kDa, RNA from Escherichia coli O157:H7)
Sigm28-transcription initiation complex with specific promoter at the state 1
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 6pmi
Q-score: 0.248
Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B
EMBO J (2020) 39 pp. e104389-e104389 [ DOI: doi:10.15252/embj.2020104389 Pubmed: 32484956 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O45:K1 (strain S88 / ExPEC))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O45:K1 (strain S88 / ExPEC))
- Rna polymerase sigma factor flia (28 kDa, Protein from Escherichia coli (strain K12))
- Synthetic nontemplate strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Nascent rna (1 kDa, RNA from Escherichia coli)
- Sigm28-transcription initiation complex with specific promoter at the state 1 (450 kDa, Complex from Escherichia coli)
Sigm28-transcription initiation complex with specific promoter at the state 2
Resolution: 3.91 Å
EM Method: Single-particle
Fitted PDBs: 6pmj
Q-score: 0.207
Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B
EMBO J (2020) 39 pp. e104389-e104389 [ DOI: doi:10.15252/embj.2020104389 Pubmed: 32484956 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O45:K1 (strain S88 / ExPEC))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O45:K1 (strain S88 / ExPEC))
- Rna polymerase sigma factor flia (28 kDa, Protein from Escherichia coli (strain K12))
- Synthetic nontemplate strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Sigm28-transcription initiation complex with specific promoter at the state 2 (450 kDa, Complex from Escherichia coli)
- Nascent rna (1 kDa, RNA from Escherichia coli)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 6pb4
Q-score: 0.224
Shi W, Jiang Y, Deng Y, Dong Z, Liu B
PLoS Biol (2020) 18 pp. e3000706- [ DOI: doi:10.1371/journal.pbio.3000706 ]
- The e. coli class-ii cap-dependent transcription activation complex with de novo rna transcript at the state 2 (550 kDa, Complex from Escherichia coli)
- Synthetic nontemplate strand dna (78-mer) (23 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Camp-activated global transcriptional regulator crp (23 kDa, Protein from Escherichia coli)
- Adenosine-3',5'-cyclic-monophosphate (329 Da, Ligand)
- Dna/rna (Complex)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Synthetic template strand dna (78-mer) (24 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha, dna-directed rna polymerase subunit beta, dna-directed rna polymerase subunit beta', dna-directed rna polymerase subunit omega, rna polymerase sigma factor rpod, camp-activated global transcriptional regulator crp (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Nascent rna (1 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)