DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Contributing Org.:
Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
OSTI Identifier:
1263688
Alternate Identifier(s):
OSTI ID: 1208686; OSTI ID: 1250981
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Published Article
Journal Name:
Molecular Cell
Additional Journal Information:
Journal Name: Molecular Cell Journal Volume: 59 Journal Issue: 2; Journal ID: ISSN 1097-2765
Publisher:
Cell Press - Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Barnes, Christopher O., Calero, Monica, Malik, Indranil, Graham, Brian W., Spahr, Henrik, Lin, Guowu, Cohen, Aina E., Brown, Ian S., Zhang, Qiangmin, Pullara, Filippo, Trakselis, Michael A., Kaplan, Craig D., and Calero, Guillermo. Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. United States: N. p., 2015. Web. doi:10.1016/j.molcel.2015.06.034.
Barnes, Christopher O., Calero, Monica, Malik, Indranil, Graham, Brian W., Spahr, Henrik, Lin, Guowu, Cohen, Aina E., Brown, Ian S., Zhang, Qiangmin, Pullara, Filippo, Trakselis, Michael A., Kaplan, Craig D., & Calero, Guillermo. Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. United States. https://doi.org/10.1016/j.molcel.2015.06.034
Barnes, Christopher O., Calero, Monica, Malik, Indranil, Graham, Brian W., Spahr, Henrik, Lin, Guowu, Cohen, Aina E., Brown, Ian S., Zhang, Qiangmin, Pullara, Filippo, Trakselis, Michael A., Kaplan, Craig D., and Calero, Guillermo. Wed . "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble". United States. https://doi.org/10.1016/j.molcel.2015.06.034.
@article{osti_1263688,
title = {Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble},
author = {Barnes, Christopher O. and Calero, Monica and Malik, Indranil and Graham, Brian W. and Spahr, Henrik and Lin, Guowu and Cohen, Aina E. and Brown, Ian S. and Zhang, Qiangmin and Pullara, Filippo and Trakselis, Michael A. and Kaplan, Craig D. and Calero, Guillermo},
abstractNote = {},
doi = {10.1016/j.molcel.2015.06.034},
journal = {Molecular Cell},
number = 2,
volume = 59,
place = {United States},
year = {Wed Jul 01 00:00:00 EDT 2015},
month = {Wed Jul 01 00:00:00 EDT 2015}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.molcel.2015.06.034

Citation Metrics:
Cited by: 71 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The Role of the Transcription Bubble and TFIIB in Promoter Clearance by RNA Polymerase II
journal, July 2005


Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution
journal, May 2009


RNA polymerase and transcription elongation factor Spt4/5 complex structure
journal, December 2010

  • Klein, B. J.; Bose, D.; Baker, K. J.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 2
  • DOI: 10.1073/pnas.1013828108

Linking Crystallographic Model and Data Quality
journal, May 2012


Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis
journal, June 2010

  • Yuzenkova, Y.; Zenkin, N.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 24
  • DOI: 10.1073/pnas.0914424107

Electrostatics of nanosystems: Application to microtubules and the ribosome
journal, August 2001

  • Baker, N. A.; Sept, D.; Joseph, S.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041
  • DOI: 10.1073/pnas.181342398

Structural basis of initial RNA polymerase II transcription: Initial RNA Pol II transcription
journal, November 2011

  • Cheung, Alan C. M.; Sainsbury, Sarah; Cramer, Patrick
  • The EMBO Journal, Vol. 30, Issue 23
  • DOI: 10.1038/emboj.2011.396

RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation
journal, October 2010


Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

RNA polymerase I structure and transcription regulation
journal, October 2013

  • Engel, Christoph; Sainsbury, Sarah; Cheung, Alan C.
  • Nature, Vol. 502, Issue 7473
  • DOI: 10.1038/nature12712

Structure of human mitochondrial RNA polymerase elongation complex
journal, October 2013

  • Schwinghammer, Kathrin; Cheung, Alan C. M.; Morozov, Yaroslav I.
  • Nature Structural & Molecular Biology, Vol. 20, Issue 11
  • DOI: 10.1038/nsmb.2683

Promoter clearance by RNA polymerase II
journal, January 2013


Structural Organization of the RNA Polymerase-Promoter Open Complex
journal, June 2000


The RNA polymerase trigger loop functions in all three phases of the transcription cycle
journal, June 2013

  • Fouqueau, T.; Zeller, M. E.; Cheung, A. C.
  • Nucleic Acids Research, Vol. 41, Issue 14
  • DOI: 10.1093/nar/gkt433

Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution
journal, May 2009

  • Spahr, H.; Calero, G.; Bushnell, D. A.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 23
  • DOI: 10.1073/pnas.0903361106

Refinement of severely incomplete structures with maximum likelihood in BUSTER–TNT
journal, November 2004

  • Blanc, E.; Roversi, P.; Vonrhein, C.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12
  • DOI: 10.1107/S0907444904016427

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
journal, September 1998

  • Brünger, A. T.; Adams, P. D.; Clore, G. M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5
  • DOI: 10.1107/S0907444998003254

The RNA Polymerase II Trigger Loop Functions in Substrate Selection and Is Directly Targeted by α-Amanitin
journal, June 2008


A Structural Model of Transcription Elongation
journal, July 2000


Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae
journal, January 2013


Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching
journal, November 2006


Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
journal, November 2006


RNA polymerase II–TFIIB structure and mechanism of transcription initiation
journal, October 2009

  • Kostrewa, Dirk; Zeller, Mirijam E.; Armache, Karim-Jean
  • Nature, Vol. 462, Issue 7271
  • DOI: 10.1038/nature08548

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex
journal, November 2012

  • Sainsbury, Sarah; Niesser, Jürgen; Cramer, Patrick
  • Nature, Vol. 493, Issue 7432
  • DOI: 10.1038/nature11715

Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase
journal, May 2001


Structural visualization of key steps in human transcription initiation
journal, February 2013


Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble
journal, May 2015


Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase
journal, January 2001

  • Harada, Yoshie; Ohara, Osamu; Takatsuki, Akira
  • Nature, Vol. 409, Issue 6816
  • DOI: 10.1038/35051126

Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis
journal, December 2006


Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity: RNA polymerase-Spt4/5 complex architecture
journal, March 2011

  • Martinez-Rucobo, Fuensanta W.; Sainsbury, Sarah; Cheung, Alan CM
  • The EMBO Journal, Vol. 30, Issue 7
  • DOI: 10.1038/emboj.2011.64

Structural Basis of Transcription Initiation
journal, October 2012


Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS
journal, December 2004


The X-ray crystal structure of RNA polymerase from Archaea
journal, January 2008

  • Hirata, Akira; Klein, Brianna J.; Murakami, Katsuhiko S.
  • Nature, Vol. 451, Issue 7180
  • DOI: 10.1038/nature06530

Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism
journal, November 2009


Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation
journal, January 2011

  • Nechaev, Sergei; Adelman, Karen
  • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1809, Issue 1
  • DOI: 10.1016/j.bbagrm.2010.11.001

Initiation Complex Structure and Promoter Proofreading
journal, July 2011


Functional analysis of Thermus thermophilus transcription factor NusG
journal, July 2010

  • Sevostyanova, A.; Artsimovitch, I.
  • Nucleic Acids Research, Vol. 38, Issue 21
  • DOI: 10.1093/nar/gkq623

Dynamic Architecture of a Minimal RNA Polymerase II Open Promoter Complex
journal, April 2012


Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination
journal, January 2013


Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation
journal, June 2008

  • Brueckner, Florian; Cramer, Patrick
  • Nature Structural & Molecular Biology, Vol. 15, Issue 8
  • DOI: 10.1038/nsmb.1458

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Dissection of Pol II Trigger Loop Function and Pol II Activity–Dependent Control of Start Site Selection In Vivo
journal, April 2012


Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage
journal, August 2003


From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II
journal, August 2013


Conserved architecture of the core RNA polymerase II initiation complex
journal, July 2014

  • Mühlbacher, Wolfgang; Sainsbury, Sarah; Hemann, Matthias
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5310

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
journal, January 2012

  • Kireeva, Maria L.; Opron, Kristopher; Seibold, Steve A.
  • BMC Biophysics, Vol. 5, Issue 1
  • DOI: 10.1186/2046-1682-5-11

Structural basis for transcription elongation by bacterial RNA polymerase
journal, June 2007

  • Vassylyev, Dmitry G.; Vassylyeva, Marina N.; Perederina, Anna
  • Nature, Vol. 448, Issue 7150
  • DOI: 10.1038/nature05932

Multisubunit RNA Polymerases Melt Only a Single DNA Base Pair Downstream of the Active Site*
journal, July 2007

  • Kashkina, Ekaterina; Anikin, Michael; Brueckner, Florian
  • Journal of Biological Chemistry, Vol. 282, Issue 30
  • DOI: 10.1074/jbc.C700098200

Structure of the 12-Subunit RNA Polymerase II Refined with the Aid of Anomalous Diffraction Data
journal, March 2009

  • Meyer, Peter A.; Ye, Ping; Suh, Man-Hee
  • Journal of Biological Chemistry, Vol. 284, Issue 19
  • DOI: 10.1074/jbc.M809199200

Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II
journal, April 2012

  • Larson, M. H.; Zhou, J.; Kaplan, C. D.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 17
  • DOI: 10.1073/pnas.1200939109

Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II
journal, February 2004


Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms
journal, February 2004


RNA Polymerase II/TFIIF Structure and Conserved Organization of the Initiation Complex
journal, October 2003


A Ratchet Mechanism of Transcription Elongation and Its Control
journal, January 2005


Structural basis of RNA polymerase II backtracking, arrest and reactivation
journal, February 2011


A general path for large-scale solubilization of cellular proteins: From membrane receptors to multiprotein complexes
journal, February 2013

  • Pullara, Filippo; Guerrero-Santoro, Jennifer; Calero, Monica
  • Protein Expression and Purification, Vol. 87, Issue 2
  • DOI: 10.1016/j.pep.2012.10.007

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Mutations in the Saccharomyces cerevisiae RPB1 Gene Conferring Hypersensitivity to 6-Azauracil
journal, March 2006