6UPX
| RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 1 | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Oh, J, Wang, D. | Deposit date: | 2019-10-18 | Release date: | 2020-06-10 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
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6UQ2
| RNA polymerase II elongation complex with dG in state 1 | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Oh, J, Wang, D. | Deposit date: | 2019-10-18 | Release date: | 2020-06-10 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
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6UQ0
| RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4 | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Oh, J, Wang, D. | Deposit date: | 2019-10-18 | Release date: | 2020-06-10 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.56 Å) | Cite: | RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
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6UQ1
| RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 6 | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Oh, J, Wang, D. | Deposit date: | 2019-10-18 | Release date: | 2020-06-10 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.6 Å) | Cite: | RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
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6EXV
| Structure of mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin | Descriptor: | AMATOXIN, DNA (25-MER), DNA (36-MER), ... | Authors: | Liu, X, Farnung, L, Wigge, C, Cramer, P. | Deposit date: | 2017-11-09 | Release date: | 2018-03-21 | Last modified: | 2019-12-11 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by alpha-amanitin. J. Biol. Chem., 293, 2018
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8S5N
| RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt | Descriptor: | DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Zhan, Y, Grabbe, F, Oberbeckmann, E, Dienemann, C, Cramer, P. | Deposit date: | 2024-02-24 | Release date: | 2024-04-10 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Three-step mechanism of promoter escape by RNA polymerase II. Mol.Cell, 84, 2024
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7WBW
| RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Osumi, K, Kujirai, T, Ehara, H, Sekine, S, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2021-12-17 | Release date: | 2023-07-05 | Method: | ELECTRON MICROSCOPY (7.1 Å) | Cite: | Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. J.Mol.Biol., 435, 2023
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7WBV
| RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome | Descriptor: | DNA (159-MER), DNA (198-MER), DNA-directed RNA polymerase subunit, ... | Authors: | Osumi, K, Kujirai, T, Ehara, H, Sekine, S, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2021-12-17 | Release date: | 2023-07-05 | Method: | ELECTRON MICROSCOPY (4.1 Å) | Cite: | Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. J.Mol.Biol., 435, 2023
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7WBX
| RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Osumi, K, Kujirai, T, Ehara, H, Sekine, S, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2021-12-17 | Release date: | 2023-07-05 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. J.Mol.Biol., 435, 2023
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4A93
| RNA Polymerase II elongation complex containing a CPD Lesion | Descriptor: | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*T*TTP*TP*TP*CP*C BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP*AP)-3', ... | Authors: | Walmacq, C, Cheung, A.C.M, Kireeva, M.L, Lubkowska, L, Ye, C, Gotte, D, Strathern, J.N, Carell, T, Cramer, P, Kashlev, M. | Deposit date: | 2011-11-23 | Release date: | 2012-03-21 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | Mechanism of Translesion Transcription by RNA Polymerase II and its Role in Cellular Resistance to DNA Damage. Mol.Cell, 46, 2012
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6INQ
| RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) | Descriptor: | DNA (198-MER), DNA (31-MER), DNA-directed RNA polymerase subunit, ... | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | Deposit date: | 2018-10-26 | Release date: | 2019-04-03 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (6.9 Å) | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage. Science, 362, 2018
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8UKR
| RNA polymerase II elongation complex with Fapy-dG lesion soaking with ATP before chemistry | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | Authors: | Hou, P, Oh, J, Wang, D. | Deposit date: | 2023-10-15 | Release date: | 2024-04-24 | Method: | X-RAY DIFFRACTION (3.78 Å) | Cite: | Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J.Am.Chem.Soc., 146, 2024
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8UKU
| RNA polymerase II elongation complex with Fapy-dG lesion with CMP added | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Hou, P, Oh, J, Wang, D. | Deposit date: | 2023-10-15 | Release date: | 2024-04-24 | Method: | X-RAY DIFFRACTION (3.6 Å) | Cite: | Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J.Am.Chem.Soc., 146, 2024
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8UKT
| RNA polymerase II elongation complex with Fapy-dG lesion with AMP added | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Hou, P, Oh, J, Wang, D. | Deposit date: | 2023-10-15 | Release date: | 2024-04-24 | Method: | X-RAY DIFFRACTION (3.6 Å) | Cite: | Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J.Am.Chem.Soc., 146, 2024
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8UKQ
| RNA polymerase II elongation complex with Fapy-dG lesion in apo state | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Hou, P, Oh, J, Wang, D. | Deposit date: | 2023-10-15 | Release date: | 2024-04-24 | Method: | X-RAY DIFFRACTION (3.5 Å) | Cite: | Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J.Am.Chem.Soc., 146, 2024
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8UKS
| RNA polymerase II elongation complex with Fapy-dG lesion soaking with CTP before chemistry | Descriptor: | CYTIDINE-5'-TRIPHOSPHATE, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | Authors: | Hou, P, Oh, J, Wang, D. | Deposit date: | 2023-10-15 | Release date: | 2024-04-24 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J.Am.Chem.Soc., 146, 2024
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3H0G
| RNA Polymerase II from Schizosaccharomyces pombe | Descriptor: | DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Spahr, H, Calero, G, Bushnell, D.A, Kornberg, R.D. | Deposit date: | 2009-04-09 | Release date: | 2009-08-25 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (3.65 Å) | Cite: | Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution. Proc.Natl.Acad.Sci.USA, 106, 2009
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8S54
| RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite structure) | Descriptor: | DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Zhan, Y, Grabber, F, Oberbeckmann, E, Dienemann, C, Cramer, P. | Deposit date: | 2024-02-22 | Release date: | 2024-04-17 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Three-step mechanism of promoter escape by RNA polymerase II. Mol.Cell, 84, 2024
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8S52
| RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt | Descriptor: | DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Zhan, Y, Grabbe, F, Oberbeckmann, E, Dienemann, C, Cramer, P. | Deposit date: | 2024-02-22 | Release date: | 2024-04-17 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Three-step mechanism of promoter escape by RNA polymerase II. Mol.Cell, 84, 2024
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8S51
| RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt | Descriptor: | DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Zhan, Y, Grabbe, F, Oberbeckmann, E, Dienemann, C, Cramer, P. | Deposit date: | 2024-02-22 | Release date: | 2024-04-17 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.1 Å) | Cite: | Three-step mechanism of promoter escape by RNA polymerase II. Mol.Cell, 84, 2024
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8S55
| RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) | Descriptor: | DNA-directed RNA polymerase II subunit E, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Zhan, Y, Grabbe, F, Oberbeckmann, E, Dienemann, C, Cramer, P. | Deposit date: | 2024-02-22 | Release date: | 2024-04-17 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Three-step mechanism of promoter escape by RNA polymerase II. Mol.Cell, 84, 2024
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3FKI
| 12-Subunit RNA Polymerase II Refined with Zn-SAD data | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | Authors: | Meyer, P.A, Ye, P, Suh, M.H, Zhang, M, Fu, J. | Deposit date: | 2008-12-16 | Release date: | 2009-03-10 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (3.88 Å) | Cite: | Structure of the 12-Subunit RNA Polymerase II Refined with the Aid of Anomalous Diffraction Data J.Biol.Chem., 284, 2009
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7ML1
| RNA polymerase II pre-initiation complex (PIC2) | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | Deposit date: | 2021-04-27 | Release date: | 2022-02-02 | Last modified: | 2022-02-16 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol.Cell, 82, 2022
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7ML2
| RNA polymerase II pre-initiation complex (PIC3) | Descriptor: | BJ4_G0004860.mRNA.1.CDS.1, BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, ... | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | Deposit date: | 2021-04-27 | Release date: | 2022-02-02 | Last modified: | 2022-02-16 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol.Cell, 82, 2022
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7ML4
| RNA polymerase II initially transcribing complex (ITC) | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | Deposit date: | 2021-04-27 | Release date: | 2022-02-02 | Last modified: | 2022-03-09 | Method: | ELECTRON MICROSCOPY (3.1 Å) | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Mol.Cell, 82, 2022
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