PDB: 13413 resultsInfo pagesStatus searchChemie searchBIRD

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6BM2	Pol II elongation complex with an abasic lesion at i-1 position Descriptor: DNA (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-13 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.403 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6BQF	Pol II elongation complex with 'dT-AP' at i+1, i-1 position Descriptor: DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-27 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.35 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6BLP	Pol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP Descriptor: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-11 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.203 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
6BLO	Pol II elongation complex with an abasic lesion at i+1 position Descriptor: DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-10 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.401 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
8EHQ	Mycobacterium tuberculosis paused transcription complex with Bacillus subtilis NusG Descriptor: DNA (38-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Vishwakarma, R.K, Murakami, K.S. Deposit date: 2022-09-14 Release date: 2023-02-01 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (3 Å) Cite: Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Proc.Natl.Acad.Sci.USA, 120, 2023
8EOE	Mycobacterium tuberculosis transcription elongation complex with Bacillus subtilis NusG (EC_LG) Descriptor: DNA (35-MER), DNA (38-MER), DNA-directed RNA polymerase subunit alpha, ... Authors: Vishwakarm, R.K, Murakami, K.S. Deposit date: 2022-10-03 Release date: 2023-02-01 Last modified: 2024-06-19 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Proc.Natl.Acad.Sci.USA, 120, 2023
6P71	X-ray crystal structure of a bacterial reiterative transcription complex of pyrBI promoter Descriptor: DNA (5'-D(*TP*AP*TP*AP*AP*TP*CP*GP*AP*GP*CP*CP*GP*GP*GP*A)-3'), DNA (5'-D(P*CP*TP*CP*CP*CP*GP*GP*CP*AP*AP*AP*TP*TP*GP*T)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Shin, Y, Murakami, K.S. Deposit date: 2019-06-04 Release date: 2019-07-24 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.92 Å) Cite: Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Nucleic Acids Res., 48, 2020
6OY6	X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 5 min Descriptor: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*GP*AP*TP*CP*TP*GP*AP*TP*GP*CP*AP*GP*G)-3'), DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Shin, Y, Murakami, K.S. Deposit date: 2019-05-14 Release date: 2019-06-19 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.096 Å) Cite: Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Nucleic Acids Res., 48, 2020
6OY5	X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 min Descriptor: DNA (5'-D(*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*CP*TP*CP*TP*GP*AP*TP*GP*CP*AP*G)-3'), DNA (5'-D(P*CP*CP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*AP*T)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Shin, Y, Murakami, K.S. Deposit date: 2019-05-14 Release date: 2019-06-05 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Nucleic Acids Res., 48, 2020
6OVR	X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter variant -1G Descriptor: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*GP*G)-3'), DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*GP*AP*AP*A)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Shin, Y, Murakami, K.S. Deposit date: 2019-05-08 Release date: 2019-07-24 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.843 Å) Cite: Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Nucleic Acids Res., 48, 2020
6OW3	X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter variant -1T Descriptor: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*GP*AP*TP*CP*TP*GP*AP*TP*GP*C)-3'), DNA (5'-D(P*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*TP*AP*AP*A)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Shin, Y, Murakami, K.S. Deposit date: 2019-05-09 Release date: 2019-07-24 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.766 Å) Cite: Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Nucleic Acids Res., 48, 2020
8P0N	Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex shallow conformation Descriptor: DNA-directed RNA polymerase 133 kDa polypeptide, DNA-directed RNA polymerase 147 kDa polypeptide, DNA-directed RNA polymerase 18 kDa subunit, ... Authors: Grimm, C, Jungwirth, S, Fischer, U. Deposit date: 2023-05-10 Release date: 2024-05-22 Method: ELECTRON MICROSCOPY (2.58 Å) Cite: Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target) To Be Published
8P0J	Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex Descriptor: DNA-directed RNA polymerase 133 kDa polypeptide, DNA-directed RNA polymerase 147 kDa polypeptide, DNA-directed RNA polymerase 18 kDa subunit, ... Authors: Grimm, C, Jungwirth, S, Fischer, U. Deposit date: 2023-05-10 Release date: 2024-05-22 Method: ELECTRON MICROSCOPY (2.39 Å) Cite: Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target) To Be Published
7W9S	Crystal structure of the enterovirus 71 polymerase elongation complex (C1S3 form) Descriptor: CYTIDINE-5'-TRIPHOSPHATE, Genome polyprotein, MAGNESIUM ION, ... Authors: Wang, M, Gong, P. Deposit date: 2021-12-10 Release date: 2022-11-16 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.53 Å) Cite: Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis. Nucleic Acids Res., 50, 2022
5W51	Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP Descriptor: 14mer non-template DNA, 29mer template DNA, 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine, ... Authors: Wang, W, Wang, D. Deposit date: 2017-06-13 Release date: 2018-06-20 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (3.404 Å) Cite: Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing. J.Am.Chem.Soc., 139, 2017
5W4U	Pol II elongation complex with an N6-methyladenine-containing template Descriptor: 14mer non-template DNA, 29mer template DNA, 9mer RNA, ... Authors: Wang, W, Wang, D. Deposit date: 2017-06-13 Release date: 2018-06-20 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (3.6 Å) Cite: Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing. J.Am.Chem.Soc., 139, 2017
8P0K	Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex, module 2 of capping enzyme mobile Descriptor: DNA-directed RNA polymerase 133 kDa polypeptide, DNA-directed RNA polymerase 147 kDa polypeptide, DNA-directed RNA polymerase 18 kDa subunit, ... Authors: Grimm, C, Jungwirth, S, Fischer, U. Deposit date: 2023-05-10 Release date: 2024-05-22 Method: ELECTRON MICROSCOPY (2.64 Å) Cite: Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target) To Be Published
7EU0	The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex Descriptor: DNA (33-MER), DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*GP*AP*GP*TP*G)-3'), DNA-directed RNA polymerase IV subunit 1, ... Authors: Fang, C.L, Wu, X.X, Huang, K, Zhang, Y. Deposit date: 2021-05-15 Release date: 2021-12-29 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.16 Å) Cite: Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science, 374, 2021
7EU1	The cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme Descriptor: DNA-directed RNA polymerase IV subunit 1, DNA-directed RNA polymerases II and IV subunit 5A, DNA-directed RNA polymerases II, ... Authors: Fang, C.L, Wu, X.X, Huang, K, Zhang, Y. Deposit date: 2021-05-15 Release date: 2021-12-29 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.86 Å) Cite: Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science, 374, 2021
7XD9	Crystal Structure of Dengue Virus serotype 2 (DENV2) Polymerase Elongation Complex (CTP Form) Descriptor: CYTIDINE-5'-TRIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... Authors: Wu, J, Wang, X, Gong, P. Deposit date: 2022-03-26 Release date: 2022-12-21 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.58 Å) Cite: Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases. Proc.Natl.Acad.Sci.USA, 120, 2023
7XD8	Crystal Structure of Dengue Virus Serotype 2 (DENV2) Polymerase Elongation Complex (Native Form) Descriptor: GLYCEROL, NS5, RNA (30-mer), ... Authors: Wu, J, Wang, X, Gong, P. Deposit date: 2022-03-26 Release date: 2022-12-21 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases. Proc.Natl.Acad.Sci.USA, 120, 2023
6D90	Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1. Descriptor: 18S rRNA, 28S rRNA, 5.8S rRNA, ... Authors: Pisareva, V.P, Pisarev, A.V, Fernandez, I.S. Deposit date: 2018-04-27 Release date: 2018-06-06 Last modified: 2019-12-18 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. Elife, 7, 2018
7UBM	Transcription antitermination complex: "pre-engaged" Qlambda-loading complex Descriptor: Antitermination protein Q, DNA (52-MER), DNA (53-MER), ... Authors: Yin, Z, Ebright, R.H. Deposit date: 2022-03-15 Release date: 2022-09-28 Last modified: 2024-06-12 Method: ELECTRON MICROSCOPY (3.13 Å) Cite: In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc.Natl.Acad.Sci.USA, 119, 2022
7UBN	Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex Descriptor: Antitermination protein, DNA (52-MER), DNA (53-MER), ... Authors: Yin, Z, Ebright, R.H. Deposit date: 2022-03-15 Release date: 2022-09-28 Last modified: 2024-06-12 Method: ELECTRON MICROSCOPY (3.36 Å) Cite: In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc.Natl.Acad.Sci.USA, 119, 2022
6LSF	Crystal structure of the enterovirus 71 polymerase elongation complex (C2S6RA/C2S6RB form) Descriptor: Genome polyprotein, RNA (35-MER), RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3'), ... Authors: Wang, M, Shu, B, Jing, X, Gong, P. Deposit date: 2020-01-17 Release date: 2020-04-29 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (2.152 Å) Cite: Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures. Nat Commun, 11, 2020

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