Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution
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- Translocation by multi-subunit RNA polymerasesMaria L. Kireeva, Mikhail Kashlev, Zachary Frome Burton · 2010 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
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- Adaptive laboratory evolution of Escherichia coli under acid stressBin Du, Connor A. Olson, Anand V. Sastry, Xin De Fang, Patrick V. Phaneuf, Ke Chen, Muyao Wu, Richard Szubin, Sibei Xu, Ye Gao et al. · 2019 · Microbiology
- The Role of the Largest RNA Polymerase Subunit Lid Element in Preventing the Formation of Extended RNA-DNA HybridTatyana Naryshkina, Konstantin D. Kuznedelov, Konstantin Severinov · 2006 · Journal of Molecular Biology
- Crosslinking of DNA repair and replication proteins to DNA in cells treated with 6-thioguanine and UVAGueranger, Quentin, Kia, Azadeh, Frith, David, Karran, Peter · 2011 · Nucleic Acids Research
- TGF-β1 induces PD-1 expression in macrophages through SMAD3/STAT3 cooperative signaling in chronic inflammationZhigang Lei, Rui Tang, Wu Yu, Chenxu Mao, Weijie Xue, Junyao Shen, Jiaojiao Yu, Xiaohong Wang, Xin Qi, Chuan Wei et al. · 2024 · JCI Insight
- Structure-Based Characterization of Multiprotein ComplexesMarkus Wiederstein, Markus Gruber, Karl Frank, Francisco Melo, Manfred J. Sippl · 2014 · Structure
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- Structure of Yeast RNA Polymerase II in SolutionJohn L. Craighead, Wei‐Hau Chang, Francisco J. Asturias · 2002 · Structure
- An Rpb4/Rpb7-Like Complex in Yeast RNA Polymerase III Contains the Orthologue of Mammalian CGRP-RCPMagali Siaut, Cécile Zaros, Emilie Levivier, Maria-Laura Ferri, Magali Court, Michel Werner, Isabelle Callebaut, Pierre Thuriaux, André Sentenac, Christine Conesa · 2002 · Molecular and Cellular Biology
- Molecular Architecture and Conformational Flexibility of Human RNA Polymerase IISeth A. Kostek, Patricia Grob, Sacha De Carlo, J. Slaton Lipscomb, Florian Garczarek, Eva Nogales · 2006 · Structure
- Advances in tomography: probing the molecular architecture of cellsKaren Fridman, Asaf Mader, Monika Zwerger, Natalie Elia, Ohad Medalia · 2012 · Nature Reviews Molecular Cell Biology
- Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiaeCraig D. Kaplan · 2012 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymeraseYara X. Mejia, Evgeny Nudler, Carlos Bustamante · 2014 · Proceedings of the National Academy of Sciences
- The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibilityAnat Bashan, Ada Yonath · 2008 · Journal of Molecular Structure
- The cryo-EM resolution revolution and transcription complexesJonas Hanske, Yashar Sadian, Christoph W. Müller · 2018 · Current Opinion in Structural Biology
- Allosteric control of catalysis by the F loop of RNA polymeraseNataliya Miropolskaya, Irina Artsimovitch, Saulius Klimašauskas, Vadim Nikiforov, Andrey V. Kulbachinskiy · 2009 · Proceedings of the National Academy of Sciences
- Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approachesWah Chiu, Matthew L. Baker, Wen Jiang, Zhen Zhou · 2002 · Current Opinion in Structural Biology
- Site specific phosphorylation of yeast RNA polymerase IJochen Gerber, Alarich Reiter, Robert Steinbauer, Steffen Jakob, Claus-Dieter Kuhn, Patrick Cramer, Joachim Griesenbeck, Philipp Milkereit, Herbert Tschochner · 2007 · Nucleic Acids Research
- Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiationStéphane Lefèvre, Hélène Dumay‐Odelot, Leyla El Ayoubi, Aidan Budd, Pierre Legrand, Noël Pinaud, Martin Teichmann, Sébastien Fribourg · 2011 · Nature Structural & Molecular Biology
- The T Body, a New Cytoplasmic RNA Granule in Saccharomyces cerevisiaeFrancisco Malagón, Torben Heick Jensen · 2008 · Molecular and Cellular Biology
- Phenotypic spectrum of POLR3B mutations: isolated hypogonadotropic hypogonadism without neurological or dental anomaliesMary Richards, Lacey Plummer, Yee-Ming Chan, Margaret Flynn Lippincott, Richard Quinton, Philip Kumanov, Stephanie Beth Seminara · 2016 · Journal of Medical Genetics
- Conserved DNA sequence features underlie pervasive RNA polymerase pausingMartyna Gajos, Olga Jasnovidova, Alena van Bömmel, Susanne Freier, Martin Vingron, Andreas Mayer · 2021 · Nucleic Acids Research
- Functional interaction of the subunit 3 of RNA polymerase II (RPB3) with transcription factor‐4 (ATF4)Roberta De Angelis, Simona Iezzi, Tiziana Bruno, Nicoletta Corbi, Monica Di Padova, Aristide Floridi, Maurizio Fanciulli, Claudio Passananti · 2003 · FEBS Letters
- Fluorescence Resonance Energy Transfer (FRET) in Analysis of Transcription-Complex Structure and FunctionJayanta Mukhopadhyay, Vladimir M. Mekler, Ekaterine Kortkhonjia, Achillefs N. Kapanidis, Yon W. Ebright, Richard H. Ebright · 2003 · Methods in enzymology on CD-ROM/Methods in enzymology
- An Integrated Chemical Cross-linking and Mass Spectrometry Approach to Study Protein Complex Architecture and FunctionJie Luo, James Fishburn, Steven Hahn, Jeffrey A. Ranish · 2011 · Molecular & Cellular Proteomics
- Protein structure determination by electron cryo-microscopySlavica Jonić, Catherine Vénien‐Bryan · 2009 · Current Opinion in Pharmacology
- Downstream DNA Selectively Affects a Paused Conformation of Human RNA Polymerase IIMurali Palangat, Chris Todd Hittinger, Robert C. Landick · 2004 · Journal of Molecular Biology
- Normal-Mode Analysis Suggests Protein Flexibility Modulation throughout RNA Polymerase's Functional CycleAdam W. Van Wynsberghe, Guohui Li, Qiang Cui · 2004 · Biochemistry
- RNA Polymerase II Transcription Complexes May Become Arrested If the Nascent RNA Is Shortened to Less than 50 NucleotidesAndrea Uájvári, Mahadeb Pal, Donal S. Luse · 2002 · Journal of Biological Chemistry
- Transcription elongation by RNA polymerase IIGrant A. Hartzog · 2003 · Current Opinion in Genetics & Development
- Structure of Human J-type Co-chaperone HscB Reveals a Tetracysteine Metal-binding DomainEduard Bitto, C.A. Bingman, Lenka Bittova, D.A. Kondrashov, Ryan M. Bannen, Brian G. Fox, John L. Markley, George N. Phillips · 2008 · Journal of Biological Chemistry
- MicroRNA profiles and their control of male gametophyte development in ricePeng Hua, Jun Chun, Taobo Ai, Yong-ao Tong, Rong Zhang, Mingming Zhao, Fang Chen, Shenghua Wang · 2012 · Plant Molecular Biology
- Ab Initio Structure Determination from Electron Microscopic Images of Single Molecules Coexisting in Different Functional StatesDominika Elmlund, Ralph Davis, Hans Elmlund · 2010 · Structure
- Intra-nuclear mobility and target search mechanisms of transcription factors: A single-molecule perspective on gene expressionDavide Normanno, Maxime Dahan, Xavier Darzacq · 2012 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing EnzymesVito Genna, Matteo Colombo, Marco De Vivo, Marco Marcia · 2017 · Structure
- Structure and function of virion RNA polymerase of a crAss-like phageDrobysheva, Arina V., Panafidina, Sofia A., Kolesnik, Matvei V., Klimuk, Evgeny I., Minakhin, Leonid, Yakunina, Maria V., Borukhov, Sergei, Nilsson, Emelie, Holmfeldt, Karin, Yutin, Natalya et al. · 2021 · Nature
- The mono-ADP-ribosyltransferases Alt and ModB of bacteriophage T4: Target proteins identifiedReinhard Depping, Christiane Lohaus, Helmut E. Meyer, Wolfgang Rüger · 2005 · Biochemical and Biophysical Research Communications
- Functions of Saccharomyces cerevisiae TFIIF during Transcription Start Site UtilizationDenys A. Khaperskyy, Michelle L. Ammerman, Robert C. Majovski, Alfred S. Ponticelli · 2008 · Molecular and Cellular Biology
- Active-Site Dynamics in RNA PolymerasesRobert C. Landick · 2004 · Cell
- Molecular Epidemiology of Mutations in Antimicrobial Resistance Loci of Pseudomonas aeruginosa Isolates from Airways of Cystic Fibrosis PatientsLeonie Greipel, Sebastian Fischer, Jens Klockgether, Marie Dorda, Samira Mielke, Lutz Wiehlmann, Nina Cramer, Burkhard Tümmler · 2016 · Antimicrobial Agents and Chemotherapy
- Transcription initiation factor TBP: old friend new questionsKevin Kramm, Christoph Engel, Dina Grohmann · 2019 · Biochemical Society Transactions
- The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGppDiego Duchi, Abhishek Mazumder, Anssi M. Malinen, Richard H. Ebright, Achillefs N. Kapanidis · 2018 · Nucleic Acids Research
- RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunitPaula Allepuz‐Fuster, Michael J O’Brien, Noelia González-Polo, Bianca Pereira, Zuzer Dhoondia, Athar Ansari, Olga Calvo · 2019 · Nucleic Acids Research
- The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional ImplicationsBasil J. Greber, Eva Nogales · 2019 · Sub-cellular biochemistry/Subcellular biochemistry
- Mediator Influences Schizosaccharomyces pombe RNA Polymerase II-dependent Transcription in VitroHenrik Spåhr, Olga Khorosjutina, Vera Baraznenok, Tomas Linder, Camilla O. Samuelsen, Damien Hermand, Tomi P. Mäkelä, Steen Holmberg, Claes M. Gustafsson · 2003 · Journal of Biological Chemistry
- Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complexMaría Ángeles Freire-Picos · 2005 · Nucleic Acids Research
- Rtr1 Is the Saccharomyces cerevisiae Homolog of a Novel Family of RNA Polymerase II-Binding ProteinsPatrick A. Gibney, Thomas Fries, Susanne M. Bailer, Kevin A. Morano · 2008 · Eukaryotic Cell
- RNA Polymerase I-Specific Subunit CAST/hPAF49 Has aRole in the Activation of Transcription by UpstreamBinding FactorKostya I. Panov, Tatiana B. Panova, Olivier Gadal, Kaori Nishiyama, Takashi Saito, Jackie Russell, Joost C.B.M. Zomerdijk · 2006 · Molecular and Cellular Biology