The cryo-EM map of TIC-TIEA complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8k59
Q-score: 0.337
Zhang KN, Liu Y, Chen M, Wang Y, Lin W, Li M, Zhang X, Gao Y, Gong Q, Chen H, Steve M, Li S, Zhang K, Liu B
To Be Published
- The cryo-em map of tic-tiea complex (400 kDa, Complex from Escherichia coli K-12)
- Dna (63-mer) (19 kDa, DNA from Escherichia coli K-12)
- Dna (61-mer) (18 kDa, DNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Rna (5'-r(*ap*gp*gp*up*a)-3') (1 kDa, RNA from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (60 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (25 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- 15 kda rna polymerase-binding protein (14 kDa, Protein from Escherichia phage T4)
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 [ Pubmed: 38951624 DOI: doi:10.1038/s41594-024-01349-9 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1a) at the lambda pr promoter (Complex from Escherichia coli)
- (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)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
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 [ Pubmed: 38951624 DOI: doi:10.1038/s41594-024-01349-9 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- (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)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- 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)
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 [ Pubmed: 38951624 DOI: doi:10.1038/s41594-024-01349-9 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- (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)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase unwinding intermediate (i1b) at the lambda pr promoter (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Nontemplate 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 [ Pubmed: 38951624 DOI: doi:10.1038/s41594-024-01349-9 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase unwinding intermediate (i1c) at the lambda pr promoter (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Chapso (631 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8tom
Q-score: 0.253
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 [ Pubmed: 38951624 DOI: doi:10.1038/s41594-024-01349-9 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Template strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 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 omega (10 kDa, Protein from Escherichia coli (strain K12))
- Nontemplate strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Zinc ion (65 Da, Ligand)
- Escherichia coli rna polymerase closed complex intermediate at the lambda pr promoter (Complex from Escherichia coli)
- Chapso (631 Da, Ligand)
Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 8y6u
Q-score: 0.318
Biochem Biophys Res Commun (2024) 691 pp. 149327-149327 [ DOI: doi:10.1016/j.bbrc.2023.149327 Pubmed: 38039839 ]
- Template promoter dna (28 kDa, DNA from Escherichia coli)
- Glycine cleavage system transcriptional activator (34 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Non-template promoter dna (28 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- E.coli transcription initiation complex with gcva (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8u3b
Q-score: 0.454
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B
Nucleic Acids Res (2024) 52 pp. 1471-1482 [ DOI: doi:10.1093/nar/gkad1231 Pubmed: 38197271 ]
- Rna (5'-d(*(gtp))-r(p*ap*a)-3') (1 kDa, RNA from Escherichia coli)
- Nitrate/nitrite response regulator protein narl (8 kDa, Protein 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 beta' (155 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Dna (69-mer) (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- E. coli narl transcription activation complex on the year promoter (625 kDa, Complex from Escherichia coli)
- Dna (69-mer) (21 kDa, DNA from Escherichia coli)
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 ]
- Rna polymerase sigma factor rpod (69 kDa, Protein 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 beta' (155 kDa, Protein from Escherichia coli)
- Escherichia coli ceda in complex with initiation complex (520 kDa, Complex from Escherichia coli)
- Cell division activator ceda (9 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription unit ssra promoter non-template dna (26 kDa, DNA from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Transcription unit ssra promoter template dna (26 kDa, DNA from Escherichia coli)
Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8jo2
Q-score: 0.397
Lou YC, Huang HY, Yeh HH, Chiang WH, Chen C, Wu KP
Nucleic Acids Res (2023) 51 pp. 10049-10058 [ DOI: doi:10.1093/nar/gkad724 Pubmed: 37665001 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli BL21(DE3))
- Structural basis of transcriptional activation by the ompr/phob-family response regulator pmra (Complex from Escherichia coli BL21(DE3))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli BL21(DE3))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli BL21(DE3))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli BL21(DE3))
- Dna-binding transcriptional regulator basr (25 kDa, Protein from Klebsiella pneumoniae JM45)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli BL21(DE3))
- Dna (65-mer) (20 kDa, DNA from synthetic construct)
- Dna (65-mer) (20 kDa, DNA from synthetic construct)