Molecular architecture and conformational flexibility of human RNA polymerase II.

[1]  U. K. Laemmli,et al.  Relation of chromosome structure and gene expression. , 1987, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[2]  P. Hanawalt,et al.  Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene , 1987, Cell.

[3]  N. Thompson,et al.  Purification of eukaryotic RNA polymerase II by immunoaffinity chromatography. Elution of active enzyme with protein stabilizing agents from a polyol-responsive monoclonal antibody. , 1990, The Journal of biological chemistry.

[4]  R. Young,et al.  Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. , 1991, The Journal of biological chemistry.

[5]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[6]  J. Frank,et al.  The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. , 1994, Ultramicroscopy.

[7]  J. Corden,et al.  Structural studies of a synthetic peptide derived from the carboxyl‐terminal domain of RNA polymerase II , 1995, Proteins.

[8]  M van Heel,et al.  A new generation of the IMAGIC image processing system. , 1996, Journal of structural biology.

[9]  D. Bushnell,et al.  The C-terminal domain revealed in the structure of RNA polymerase II. , 1996, Journal of molecular biology.

[10]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[11]  D. Reinberg,et al.  Purification of human RNA polymerase II and general transcription factors. , 1996, Methods in enzymology.

[12]  T Lagrange,et al.  The general transcription factors of RNA polymerase II. , 1996, Genes & development.

[13]  R. Roeder,et al.  The role of general initiation factors in transcription by RNA polymerase II. , 1996, Trends in biochemical sciences.

[14]  N Grigorieff,et al.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. , 1998, Journal of molecular biology.

[15]  R. Kornberg,et al.  Electron crystallography of yeast RNA polymerase II preserved in vitreous ice. , 1998, Ultramicroscopy.

[16]  T. Steitz,et al.  Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme , 1998, The EMBO journal.

[17]  J. Dubochet,et al.  Cryo-negative staining. , 1998, Micron.

[18]  K. Severinov,et al.  Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution , 1999, Cell.

[19]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[20]  T. Steitz,et al.  Structural basis for initiation of transcription from an RNA polymerase–promoter complex , 1999, Nature.

[21]  P. Cramer,et al.  Architecture of RNA polymerase II and implications for the transcription mechanism. , 2000, Science.

[22]  R. Roeder,et al.  Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. , 2000, Trends in biochemical sciences.

[23]  M. Kashlev,et al.  The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex* , 2000, The Journal of Biological Chemistry.

[24]  P. Cramer,et al.  Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution , 2001, Science.

[25]  S Birmanns,et al.  Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. , 2001, Journal of structural biology.

[26]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[27]  P. Cramer,et al.  Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution , 2001, Science.

[28]  K. Murakami,et al.  Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex , 2002, Science.

[29]  S. Yokoyama,et al.  Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution , 2002, Nature.

[30]  P. Chacón,et al.  Multi-resolution contour-based fitting of macromolecular structures. , 2002, Journal of molecular biology.

[31]  R. Kingston,et al.  Cooperation between Complexes that Regulate Chromatin Structure and Transcription , 2002, Cell.

[32]  Francisco J Asturias,et al.  Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA. , 2002, Structure.

[33]  J. Svejstrup Transcription repair coupling factor: a very pushy enzyme. , 2002, Molecular cell.

[34]  Roger D Kornberg,et al.  Complete, 12-subunit RNA polymerase II at 4.1-Å resolution: Implications for the initiation of transcription , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  C. Carles,et al.  Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I. , 2003, Journal of molecular biology.

[36]  A. Lehmann DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. , 2003, Biochimie.

[37]  J. Svejstrup Rescue of arrested RNA polymerase II complexes , 2003, Journal of Cell Science.

[38]  R. Henderson,et al.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. , 2003, Journal of molecular biology.

[39]  P. Cramer,et al.  Architecture of initiation-competent 12-subunit RNA polymerase II , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  N. Grigorieff,et al.  Accurate determination of local defocus and specimen tilt in electron microscopy. , 2003, Journal of structural biology.

[41]  P. Cramer,et al.  Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage , 2003, Cell.

[42]  N. Grigorieff,et al.  Noise bias in the refinement of structures derived from single particles. , 2004, Ultramicroscopy.

[43]  Roger D Kornberg,et al.  Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms , 2004, Science.

[44]  D. Lane,et al.  Transcription — guarding the genome by sensing DNA damage , 2004, Nature Reviews Cancer.

[45]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[46]  High-resolution protein-DNA contacts for the yeast RNA polymerase II general transcription machinery. , 2004, Biochemistry.

[47]  P. Cramer,et al.  Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. , 2004, Molecular cell.

[48]  Francisco J Asturias,et al.  RNA polymerase II structure, and organization of the preinitiation complex. , 2004, Current opinion in structural biology.

[49]  E. Nogales,et al.  Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome. , 2005, Molecular cell.

[50]  Finn Werner,et al.  Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II , 2005, Nucleic acids research.

[51]  Anton Meinhart,et al.  Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7* , 2005, Journal of Biological Chemistry.

[52]  J. Frank,et al.  A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. , 2006, Journal of structural biology.

[53]  Pawel A Penczek,et al.  Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. , 2006, Structure.

[54]  Chao Yang,et al.  Estimation of variance in single-particle reconstruction using the bootstrap technique. , 2006, Journal of Structural Biology.