PDB: 8865 resultsInfo pagesStatus searchChemie searchBIRD

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2NVZ	RNA Polymerase II elongation complex with UTP, updated 11/2006 Descriptor: 28-MER DNA template strand, 5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3', 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3', ... Authors: Wang, D, Bushnell, D.A, Westover, K.D, Kaplan, C.D, Kornberg, R.D. Deposit date: 2006-11-14 Release date: 2006-12-19 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (4.3 Å) Cite: Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell(Cambridge,Mass.), 127, 2006
2NVX	RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP Descriptor: 28-MER DNA template strand, 5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3', 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3', ... Authors: Wang, D, Bushnell, D.A, Westover, K.D, Kaplan, C.D, Kornberg, R.D. Deposit date: 2006-11-13 Release date: 2006-12-19 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (3.6 Å) Cite: Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell(Cambridge,Mass.), 127, 2006
2NVQ	RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP Descriptor: 28-MER DNA template strand, 5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3', 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3', ... Authors: Wang, D, Bushnell, D.A, Westover, K.D, Kaplan, C.D, Kornberg, R.D. Deposit date: 2006-11-13 Release date: 2006-12-12 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell(Cambridge,Mass.), 127, 2006
2NVT	RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP Descriptor: 5'-D(*GP*TP*AP*CP*TP*TP*G)-3', 5'-D(P*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*T)-3', 5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3', ... Authors: Wang, D, Bushnell, D.A, Westover, K.D, Kaplan, C.D, Kornberg, R.D. Deposit date: 2006-11-13 Release date: 2006-12-12 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (3.36 Å) Cite: Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell(Cambridge,Mass.), 127, 2006
2F8E	Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated VPg protein Descriptor: MAGNESIUM ION, MANGANESE (II) ION, RNA-dependent RNA polymerase, ... Authors: Ferrer-Orta, C, Arias, A, Perez-Luque, R, Escarmis, C, Domingo, E, Verdaguer, N. Deposit date: 2005-12-02 Release date: 2006-03-28 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.9 Å) Cite: The structure of a protein primer-polymerase complex in the initiation of genome replication Embo J., 25, 2006
6YYS	Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Kouba, T, Koval, T, Krasny, L, Dohnalek, J. Deposit date: 2020-05-05 Release date: 2020-11-04 Last modified: 2024-07-10 Method: ELECTRON MICROSCOPY (3.08 Å) Cite: Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. Nat Commun, 11, 2020
1YUY	HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE GENOTYPE 2a Descriptor: RNA-Dependent RNA polymerase, SULFATE ION Authors: Biswal, B.K, Cherney, M.M, Wang, M, Chan, L, Yannopoulos, C.G, Bilimoria, D, Nicolas, O, Bedard, J, James, M.N.G. Deposit date: 2005-02-14 Release date: 2005-03-22 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Crystal structures of the RNA dependent RNA polymerase genotype 2a of hepatitis C virus reveal two conformations and suggest mechanisms of inhibition by non-nucleoside inhibitors. J.Biol.Chem., 280, 2005
7F0S	A crystal structure of alphavirus nonstructural protein 4 (nsP4) reveals an intrinsically 1dynamic RNA-dependent RNA polymerase Descriptor: RNA-directed RNA polymerase nsP4 Authors: Tan, Y.B, Luo, D. Deposit date: 2021-06-06 Release date: 2022-02-16 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold. Nucleic Acids Res., 50, 2022
3P9Y	Crystal structure of the Drosophila melanogaster Ssu72-pCTD complex Descriptor: CG14216, IMIDAZOLE, TETRAETHYLENE GLYCOL, ... Authors: Werner-Allen, J.W, Zhou, P. Deposit date: 2010-10-18 Release date: 2010-12-15 Last modified: 2016-08-17 Method: X-RAY DIFFRACTION (2.1 Å) Cite: cis-Proline-mediated Ser(P)5 Dephosphorylation by the RNA Polymerase II C-terminal Domain Phosphatase Ssu72. J.Biol.Chem., 286, 2011
3TJ1	Crystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3 Descriptor: RNA polymerase I-specific transcription initiation factor RRN3 Authors: Blattner, C, Jennebach, S, Herzog, F, Mayer, A, Cheung, A.C.M, Witte, G, Lorenzen, K, Hopfner, K.-P, Heck, A.J.R, Aebersold, R, Cramer, P. Deposit date: 2011-08-23 Release date: 2011-09-28 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev., 25, 2011
2A69	Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin Descriptor: DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... Authors: Artsimovitch, I, Vassylyeva, M.N, Svetlov, D, Svetlov, V, Perederina, A, Igarashi, N, Matsugaki, N, Wakatsuki, S, Tahirov, T.H, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2005-07-02 Release date: 2005-09-20 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell(Cambridge,Mass.), 122, 2005
2A68	Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin Descriptor: DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... Authors: Artsimovitch, I, Vassylyeva, M.N, Svetlov, D, Svetlov, V, Perederina, A, Igarashi, N, Matsugaki, N, Wakatsuki, S, Tahirov, T.H, Vassylyev, D.G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2005-07-01 Release date: 2005-09-20 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell(Cambridge,Mass.), 122, 2005
2XI5	N-terminal endonuclease domain of La Crosse virus L-protein Descriptor: MANGANESE (II) ION, RNA POLYMERASE L Authors: Reguera, J, Weber, F, Cusack, S. Deposit date: 2010-06-28 Release date: 2010-10-06 Last modified: 2012-07-18 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Bunyaviridae RNA Polymerases (L-Protein) Have an N-Terminal, Influenza-Like Endonuclease Domain, Essential for Viral CAP-Dependent Transcription. Plos Pathog., 6, 2010
2XI7	N-terminal endonuclease domain of La Crosse virus L-protein Descriptor: 2-4-DIOXO-4-PHENYLBUTANOIC ACID, MANGANESE (II) ION, RNA POLYMERASE L Authors: Reguera, J, Weber, F, Cusack, S. Deposit date: 2010-06-28 Release date: 2010-10-06 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Bunyaviridae RNA Polymerases (L-Protein) Have an N-Terminal, Influenza-Like Endonuclease Domain, Essential for Viral CAP-Dependent Transcription. Plos Pathog., 6, 2010
2XP1	Structure of the tandem SH2 domains from Antonospora locustae transcription elongation factor Spt6 Descriptor: CHLORIDE ION, SPT6, SULFATE ION Authors: Diebold, M.-L, Koch, M, Cavarelli, J, Romier, C. Deposit date: 2010-08-24 Release date: 2010-09-29 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Noncanonical Tandem Sh2 Enables Interaction of Elongation Factor Spt6 with RNA Polymerase II. J.Biol.Chem., 285, 2010
7NVV	XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) Descriptor: ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, General transcription and DNA repair factor IIH helicase subunit XPB, ... Authors: Aibara, S, Schilbach, S, Cramer, P. Deposit date: 2021-03-16 Release date: 2021-05-05 Last modified: 2024-07-10 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Structures of mammalian RNA polymerase II pre-initiation complexes. Nature, 594, 2021
4M3O	Crystal structure of K.lactis Rtr1 NTD Descriptor: KLLA0F12672p, ZINC ION Authors: Hsu, P.L, Yang, W, Zheng, N, Varani, G. Deposit date: 2013-08-06 Release date: 2014-07-16 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Rtr1 Is a Dual Specificity Phosphatase That Dephosphorylates Tyr1 and Ser5 on the RNA Polymerase II CTD. J.Mol.Biol., 426, 2014
4YGX	Crystal Structure of D. melanogaster Ssu72+Symplekin bound to cis peptidomimetic CTD phospho-Ser5 peptide Descriptor: LD40846p, Symplekin, cis peptidomimetic CTD phospho-Ser5 peptide Authors: Mayfield, J.E, Zhang, Y. Deposit date: 2015-02-26 Release date: 2015-09-16 Last modified: 2015-10-28 Method: X-RAY DIFFRACTION (2.95 Å) Cite: Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. Acs Chem.Biol., 10, 2015
6IRV	Crystal structure of the human cap-specific adenosine methyltransferase Descriptor: Phosphorylated CTD-interacting factor 1 Authors: Hirano, S, Nishimasu, H, Ishitani, R, Nureki, O. Deposit date: 2018-11-14 Release date: 2018-12-05 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Cap-specific terminal N 6 -methylation of RNA by an RNA polymerase II-associated methyltransferase. Science, 363, 2019
6IRW	Crystal structure of the human cap-specific adenosine methyltransferase bound to SAH Descriptor: Phosphorylated CTD-interacting factor 1, S-ADENOSYL-L-HOMOCYSTEINE Authors: Hirano, S, Nishimasu, H, Ishitani, R, Nureki, O. Deposit date: 2018-11-14 Release date: 2018-12-05 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Cap-specific terminal N 6 -methylation of RNA by an RNA polymerase II-associated methyltransferase. Science, 363, 2019
6GMH	Structure of activated transcription complex Pol II-DSIF-PAF-SPT6 Descriptor: CDC73, CTR9,RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein CTR9 homolog, DNA-directed RNA polymerase II subunit RPB9, ... Authors: Vos, S.M, Farnung, L, Boehing, M, Linden, A, Wigge, C, Urlaub, H, Cramer, P. Deposit date: 2018-05-26 Release date: 2018-08-22 Last modified: 2019-12-18 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature, 560, 2018
8JCH	Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1 (Pol II Rat1-PTTC1) Descriptor: 5'-3' exoribonuclease 2, DNA (38-MER), DNA-directed RNA polymerase II subunit RPB1, ... Authors: Zeng, Y, Zhang, Y. Deposit date: 2023-05-11 Release date: 2024-01-31 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (2.7 Å) Cite: Structural basis of exoribonuclease-mediated mRNA transcription termination. Nature, 628, 2024
6TED	Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 Descriptor: DNA (37-MER), DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase subunit, ... Authors: Vos, S.M, Farnung, L, Cramer, P. Deposit date: 2019-11-11 Release date: 2020-07-22 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Nat.Struct.Mol.Biol., 27, 2020
7ZS9	Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Wang, H, Cramer, P. Deposit date: 2022-05-06 Release date: 2022-11-16 Last modified: 2024-07-24 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Structures of transcription preinitiation complex engaged with the +1 nucleosome. Nat.Struct.Mol.Biol., 30, 2023
7ZSB	Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Wang, H, Cramer, P. Deposit date: 2022-05-06 Release date: 2022-11-16 Last modified: 2024-07-24 Method: ELECTRON MICROSCOPY (6.6 Å) Cite: Structures of transcription preinitiation complex engaged with the +1 nucleosome. Nat.Struct.Mol.Biol., 30, 2023

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