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4KMU	X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Murakami, K.S. Deposit date: 2013-05-08 Release date: 2013-05-22 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (3.85 Å) Cite: X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins. J.Med.Chem., 56, 2013
4MEX	Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Feng, Y, Zhang, Y, Arnold, E, Ebright, R.H. Deposit date: 2013-08-27 Release date: 2014-05-21 Last modified: 2014-06-25 Method: X-RAY DIFFRACTION (3.902 Å) Cite: Transcription inhibition by the depsipeptide antibiotic salinamide A. Elife, 3, 2014
8TOE	Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter Descriptor: CHAPSO, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Darst, S.A, Saecker, R.M, Mueller, A.U. Deposit date: 2023-08-03 Release date: 2024-07-03 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol., 2024
8TO6	Escherichia coli RNA polymerase unwinding intermediate (I1d) at the lambda PR promoter Descriptor: (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, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Darst, S.A, Saecker, R.M, Mueller, A.U. Deposit date: 2023-08-02 Release date: 2024-07-03 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol., 2024
8TOM	Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter Descriptor: CHAPSO, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Darst, S.A, Saecker, R.M, Mueller, A.U. Deposit date: 2023-08-03 Release date: 2024-07-03 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol., 2024
8TO8	Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter Descriptor: (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, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Darst, S.A, Saecker, R.M, Mueller, A.U. Deposit date: 2023-08-03 Release date: 2024-07-03 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol., 2024
8TO1	Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter Descriptor: (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, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Darst, S.A, Saecker, R.M, Mueller, A.U. Deposit date: 2023-08-02 Release date: 2024-07-03 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (2.8 Å) Cite: Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol., 2024
8X6G	Cryo-EM structure of Staphylococcus aureus sigB-dependent RNAP-promoter open complex Descriptor: DNA (70-mer), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Yuan, L, Xu, L, Liu, Q, Feng, Y. Deposit date: 2023-11-21 Release date: 2024-06-05 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase. Nat Commun, 15, 2024
8X6F	Cryo-EM structure of Staphylococcus aureus sigA-dependent RNAP-promoter open complex Descriptor: DNA (71-mer), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Yuan, L, Xu, L, Liu, Q, Feng, Y. Deposit date: 2023-11-21 Release date: 2024-06-05 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase. Nat Commun, 15, 2024
8W8N	Thermus thermophilus initiation transcription complex in the pre-translocated state Descriptor: DNA (21-MER), DNA (27-MER), DNA-directed RNA polymerase subunit alpha, ... Authors: Li, L, Zhang, Y. Deposit date: 2023-09-04 Release date: 2024-07-24 Method: X-RAY DIFFRACTION (2.693 Å) Cite: Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc.Natl.Acad.Sci.USA, 121, 2024
8W8P	Thermus thermophilus initiation transcription complex containing CMPcPP in the post-translocated state Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA (21-MER), DNA (27-MER), ... Authors: Li, L, Zhang, Y. Deposit date: 2023-09-04 Release date: 2024-07-24 Method: X-RAY DIFFRACTION (3.165 Å) Cite: Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc.Natl.Acad.Sci.USA, 121, 2024
8W8O	Thermus thermophilus initiation complex in the half-translocated state Descriptor: DNA (21-MER), DNA (27-MER), DNA-directed RNA polymerase subunit alpha, ... Authors: Li, L, Zhang, Y. Deposit date: 2023-09-04 Release date: 2024-07-24 Method: X-RAY DIFFRACTION (2.512 Å) Cite: Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc.Natl.Acad.Sci.USA, 121, 2024
8Z6G	the AlgU-MucAcyto complex structure in Pseudomonas aeruginosa Descriptor: Anti sigma-E RseA, N-terminal domain protein, RNA polymerase sigma factor Authors: Li, T, Wang, Y.Z, Bao, R. Deposit date: 2024-04-19 Release date: 2024-05-08 Method: X-RAY DIFFRACTION (2.10109687 Å) Cite: the AlgU-MucAcyto complex structure in Pseudomonas aeruginosa To Be Published
8U3B	Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A Descriptor: DNA (69-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Liu, B, Kompaniiets, D, Wang, D. Deposit date: 2023-09-07 Release date: 2024-01-17 Last modified: 2024-02-21 Method: ELECTRON MICROSCOPY (3.23 Å) Cite: Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Res., 52, 2024
8Y6U	Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Lin, W, Shi, J. Deposit date: 2024-02-03 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.97 Å) Cite: NMR analysis of a loop-bulge structure of UUCGA pentaloop. Biochem.Biophys.Res.Commun., 691, 2024
7KHI	Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp Descriptor: CHAPSO, DNA (28-MER), DNA (36-MER), ... Authors: Shin, Y, Qayyum, M.Z, Murakami, K.S. Deposit date: 2020-10-21 Release date: 2020-10-28 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (3.62 Å) Cite: Structural basis of ribosomal RNA transcription regulation. Nat Commun, 12, 2021
6N4C	EM structure of the DNA wrapping in bacterial open transcription initiation complex Descriptor: DNA (94-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Florez-Ariza, A, Cassago, A, de Oliveira, P.S.L, Guerra, D.G, Portugal, R.V. Deposit date: 2018-11-19 Release date: 2020-05-27 Method: ELECTRON MICROSCOPY (17 Å) Cite: Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation Biorxiv, 2020
6N61	Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin Descriptor: 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Capistruin, ... Authors: Braffman, N, Hauver, J, Campbell, E.A, Darst, S.A. Deposit date: 2018-11-24 Release date: 2019-01-09 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.253 Å) Cite: Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc. Natl. Acad. Sci. U.S.A., 116, 2019
6N57	Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation I Descriptor: CHAPSO, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Chen, J, Chiu, C.E, Campbell, E.A, Darst, S.A. Deposit date: 2018-11-21 Release date: 2020-02-26 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation. Elife, 8, 2019
6VVS	Crystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation complex with antibiotic Sorangicin Descriptor: 1,2-ETHANEDIOL, DNA (26-MER), DNA (31-MER), ... Authors: Lilic, M, Braffman, N, Darst, S.A, Campbell, E.A. Deposit date: 2020-02-18 Release date: 2020-10-21 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.112 Å) Cite: The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. Proc.Natl.Acad.Sci.USA, 117, 2020
6WMT	F. tularensis RNAPs70-(MglA-SspA)-ppGpp-PigR-iglA DNA complex Descriptor: DNA NT-strand, DNA NT-strand downstream, DNA T-strand, ... Authors: Travis, B.A, Brennan, R.G, Schumacher, M.A. Deposit date: 2020-04-21 Release date: 2020-11-11 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (4.43 Å) Cite: Structural Basis for Virulence Activation of Francisella tularensis. Mol.Cell, 81, 2021
6N58	Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II Descriptor: CHAPSO, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Chen, J, Chiu, C.E, Campbell, E.A, Darst, S.A. Deposit date: 2018-11-21 Release date: 2020-02-26 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.78 Å) Cite: E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation. Elife, 8, 2019
6N60	Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25) Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Braffman, N, Hauver, J, Campbell, E.A, Darst, S.A. Deposit date: 2018-11-23 Release date: 2019-01-09 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.68 Å) Cite: Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc. Natl. Acad. Sci. U.S.A., 116, 2019
7L7B	Clostridioides difficile RNAP with fidaxomicin Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Boyaci, H, Campbell, E.A, Darst, S.A, Chen, J. Deposit date: 2020-12-28 Release date: 2022-02-02 Last modified: 2024-05-29 Method: ELECTRON MICROSCOPY (3.26 Å) Cite: Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature, 604, 2022
6WOX	Thermus thermophilus RNA polymerase initially transcribing complex with 2'dCTP Descriptor: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA (25-MER), DNA (5'-D(P*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*G)-3'), ... Authors: Shin, Y, Murakami, K.S. Deposit date: 2020-04-26 Release date: 2020-06-10 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (3.14 Å) Cite: The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Nat Commun, 12, 2021

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