Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8to1
Q-score: 0.477
Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA
Nat Struct Mol Biol (2024) 31 pp. 1778-1788 [ DOI: doi:10.1038/s41594-024-01349-9 Pubmed: 38951624 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Escherichia coli rna polymerase unwinding intermediate (i1a) at the lambda pr promoter (Complex from Escherichia coli)
Escherichia coli RNA polymerase unwinding intermediate (I1d) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8to6
Q-score: 0.465
Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA
Nat Struct Mol Biol (2024) 31 pp. 1778-1788 [ DOI: doi:10.1038/s41594-024-01349-9 Pubmed: 38951624 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1d) at the lambda pr promoter (Complex from Escherichia coli)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8to8
Q-score: 0.461
Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA
Nat Struct Mol Biol (2024) 31 pp. 1778-1788 [ DOI: doi:10.1038/s41594-024-01349-9 Pubmed: 38951624 ]
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Escherichia coli rna polymerase unwinding intermediate (i1b) at the lambda pr promoter (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8toe
Q-score: 0.462
Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA
Nat Struct Mol Biol (2024) 31 pp. 1778-1788 [ DOI: doi:10.1038/s41594-024-01349-9 Pubmed: 38951624 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Chapso (631 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1c) at the lambda pr promoter (Complex from Escherichia coli)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
Structure of Escherichia coli CedA in complex with transcription initiation complex
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8ftd
Q-score: 0.456
Vasilyev N, Liu MMJ, Epshtein V, Shamovsky I, Nudler E
Nat Struct Mol Biol (2024) 31 pp. 141-149 [ Pubmed: 38177674 DOI: doi:10.1038/s41594-023-01154-w ]
- Zinc ion (65 Da, Ligand)
- Transcription unit ssra promoter template dna (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (69 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli ceda in complex with initiation complex (520 kDa, Complex from Escherichia coli)
- Cell division activator ceda (9 kDa, Protein from Escherichia coli)
- Chapso (631 Da, Ligand)
- Transcription unit ssra promoter non-template dna (26 kDa, DNA from Escherichia coli)
Cryo-EM structure of 27a bound to E. coli RNAP and rrnBP1 promoter complex
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 7szk
Q-score: 0.462
Rajeswaran W, Ashkar SR, Lee PH, Yeomans L, Shin Y, Franzblau SG, Murakami KS, Showalter HD, Garcia GA
Acs Infect Dis. (2022) 8 pp. 1422-1438 [ Pubmed: 35772744 DOI: doi:10.1021/acsinfecdis.1c00636 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna (5'-d(p*cp*tp*cp*gp*tp*ap*gp*ap*gp*tp*cp*cp*gp*tp*gp*tp*cp*a)-3') (19 kDa, DNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- 27a bound to e. coli rnap and rrnbp1 promoter complex (Complex from Escherichia coli K-12)
- (2s,7r,7ar,13ap,16z,18e,20s,21s,22r,23r,24r,25s,26r,27s,28e)-5,21,23-trihydroxy-27-methoxy-2,4,16,20,22,24,26-heptamethyl-10-[4-(2-methylpropyl)piperazin-1-yl]-12-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1,6,15-trioxo-1,2,7,7a-tetrahydro-6h-2,7-(epoxypentadeca[1,11,13]trienoimino)[1]benzofuro[4,5-a]phenoxazin-25-yl acetate (1 kDa, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna (5'-d(p*cp*tp*cp*gp*tp*ap*gp*ap*gp*tp*cp*cp*gp*tp*gp*tp*cp*a)-3') (19 kDa, DNA from Escherichia coli K-12)
Cryo-EM structure of Escherichia coli RNA polymerase bound to T7A1 promoter DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7mkj
Q-score: 0.509
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Template strand of t7a1 promoter dna (27 kDa, DNA from Escherichia phage T7)
- Zinc ion (65 Da, Ligand)
- T7a1 promoter dna (Complex from Escherichia phage T7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Escherichia coli rna polymerase bound to t7a1 promoter dna (Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein 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)
- Nontemplate strand of t7a1 promoter dna (28 kDa, DNA from Escherichia phage T7)
- Rna polymerase (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
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 [ DOI: doi:10.1038/s41467-021-22990-8 Pubmed: 33976201 ]
- Ecmrr-rnap-promoter open complex (ecmrr-rpo) (Complex from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- Synthetic template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 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 [ DOI: doi:10.1038/s41467-021-22990-8 Pubmed: 33976201 ]
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli O157:H7)
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- Rna (5'-d(*(gtp))-r(p*ap*g)-3') (1 kDa, RNA 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 (150 kDa, Protein from Escherichia coli O157:H7)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Ecmrr-rnap-promoter initial transcribing complex with 3-nt rna transcript (ecmrr-rpitc-3nt) (Complex from Escherichia coli O157:H7)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- 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)
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 [ DOI: doi:10.1038/s41467-021-22990-8 Pubmed: 33976201 ]
- 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)
- Zinc ion (65 Da, Ligand)
- Ecmrr-rnap-promoter initial transcribing complex with 4-nt rna transcript (ecmrr-rpitc-4nt) (Complex from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli O157:H7)
- Tetraphenylantimonium ion (430 Da, Ligand)
- Merr family transcriptional regulator ecmrr (31 kDa, Protein from Escherichia coli O157:H7)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli O157:H7)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli O157:H7)
- Rna (5'-d(*(gtp))-r(p*cp*ap*g)-3') (1 kDa, RNA from Escherichia coli O157:H7)
- Magnesium ion (24 Da, Ligand)
- Synthetic non-template strand dna (54-mer) (16 kDa, DNA from Escherichia coli O157:H7)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli O157:H7)