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)
Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPo
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6xl6
Q-score: 0.536
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)
- Ecmrr-spacer dna complex in ecmrr-rnap-promoter open complex (ecmrr-rpo) (Complex from Escherichia coli)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
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)
Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-3nt
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6xla
Q-score: 0.546
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 ]
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli)
- Ecmrr-spacer dna complex in ecmrr-rnap-promoter initial transcribing complex with 3-nt rna transcript (ecmrr-rpitc-3nt) (Complex from Escherichia coli)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
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)
Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-4nt
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6xlk
Q-score: 0.495
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 ]
- Tetraphenylantimonium ion (430 Da, Ligand)
- Ecmrr-spacer dna complex in ecmrr-rnap-promoter initial transcribing complex with 4-nt rna transcript (ecmrr-rpitc-4nt) (Complex from Escherichia coli)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Chapso (631 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli)
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)