6DPL

Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 200 mM Rb+ for 720 s at 21 C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cation trafficking propels RNA hydrolysis.

Samara, N.L.Yang, W.

(2018) Nat. Struct. Mol. Biol. 25: 715-721

  • DOI: 10.1038/s41594-018-0099-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg <sup>2+ </sup> ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crysta ...

    Catalysis by members of the RNase H superfamily of enzymes is generally believed to require only two Mg 2+ ions that are coordinated by active-site carboxylates. By examining the catalytic process of Bacillus halodurans RNase H1 in crystallo, however, we found that the two canonical Mg 2+ ions and an additional K + failed to align the nucleophilic water for RNA cleavage. Substrate alignment and product formation required a second K + and a third Mg 2+ , which replaced the first K + and departed immediately after cleavage. A third transient Mg 2+ has also been observed for DNA synthesis, but in that case it coordinates the leaving group instead of the nucleophile as in the case of the RNase H1 hydrolysis reaction. These transient cations have no contact with the enzymes. Other DNA and RNA enzymes that catalyze consecutive cleavage and strand-transfer reactions in a single active site may similarly require cation trafficking coordinated by the substrate.


    Organizational Affiliation

    Department of biological and medical physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: dlyumkis@salk.edu.,Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, People's Republic of China.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina. Electronic address: jromero@fcq.unc.edu.ar.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France. pedro.alzari@pasteur.fr marco.bellinzoni@pasteur.fr.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.,German Cancer Consortium, DKTK , 60590 Site Frankfurt/Mainz , DE , Germany.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: ysun8@mdanderson.org.,Center for Open Research Resources & Equipment (COR2E) , University of Connecticut , 91 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina.,Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103.,Department of Neuroscience, The Scripps Research Institute, Jupiter, United States.,Institute for X-Ray Physics, University of Goettingen, 37077 Goettingen, Germany.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,3Faculty of Health Sciences, Department of Medical Biology, Research group of Host-Microbe Interactions, UiT-The Artic University of Norway, 9037 Tromsø, Norway.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), US National Institutes of Health (NIH), Bethesda, MD, USA.,CBH, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden. Electronic address: sophia@kth.se.,6Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Chemical Biology and Medicinal Chemistry, and.,Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex System, Fudan University, Shanghai, People's Republic of China.,Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.,Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. rficner@uni-goettingen.de.,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China; wenbo.ma@ucr.edu majb@fudan.edu.cn.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.,Experimental Medical Science, Medical Structural Biology, BMC C13, Lund University, SE-221 84 Lund, Sweden.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. Electronic address: smeroueh@iu.edu.,Unit of Polar Genomics , Korea Polar Research Institute , Incheon 21990 , Republic of Korea.,ESRF - The European Synchrotron, 71 Rue Jules Horowitz, F-38000 Grenoble, France.,Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland.,MacCHESS, Cornell University, Ithaca, NY 14853.,Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.,CNR-Institute of Molecular Biology and Pathology, Rome, Italy.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: margaret.phillips@utsouthwestern.edu.,Department of Chemistry, Indiana University, Bloomington, IN 47405; cedann@indiana.edu dbkearns@indiana.edu.,Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK katrin.rittinger@crick.ac.uk.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Pharmacology, Yale University, New Haven, CT, USA.,Workgroup Structural Biology of Biosynthetic Enzymes , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1 , 66123 Saarbrücken , Germany.,School of Molecular Sciences, Arizona State University, Tempe, AZ 85287.,The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore, 637551, Singapore. julien@ntu.edu.sg.,Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany.,The Max-Planck Institute of Biochemistry, Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany.,Center for Matrix Biology, Vanderbilt University Medical Center, United States.,SER-CAT and Department of Biochemistry and Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), US National Institutes of Health (NIH), Bethesda, MD, USA. wei.yang@nih.gov.,Department of Pharmaceutical Sciences , University of Connecticut , 69 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina.,the Departments of Microbiology and Immunology, and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and.,Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. sjohann1@gwdg.de.,Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. pneuman2@gwdg.de.,National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China. Electronic address: Jianggu2012@163.com.,Department of Dermatology , University Medical Center, Eberhard Karls University Tübingen , Liebermeisterstr. 25 , 72076 Tübingen , DE , Germany.,Department of Biosciences, Rice University, Houston, TX, USA.,Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany.,Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK.,Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami , Florida 33134 , United States.,Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States.,Vanderbilt University Medical Center, United States.,Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.,ENEA CR Frascati, Diagnostics and Metrology Laboratory, FSN-TECFIS-DIM, Frascati, Italy.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany.,From the Departments of Chemistry, redinbo@unc.edu.,Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore, 636921, Singapore. julien@ntu.edu.sg.,Department of Cell Biology, Yale University, New Haven, CT, USA. david.calderwood@yale.edu.,Istituto Zooprofilattico dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy.,Department of Biological Sciences Xi'an Jiaotong-Liverpool University111 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou, 215123, People's Republic of China.,Department of Physics, Simon Fraser University, Canada.,Laboratory of biomolecular NMR spectroscopy, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore, 637551, Singapore.,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel. mlandau@technion.ac.il.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA.,Simon Fraser University, Canada.,The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: baumeist@biochem.mpg.de.,Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461; denis.rousseau@einstein.yu.edu.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,a Laboratoire d'Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS , Université Paris Diderot , Paris , France.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Shanghai Medical College of Fudan University, Shanghai, People's Republic of China.,Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), US National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Biochemistry and Biophysics, and.,Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.,b Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS , Université Paris Descartes , Paris , France.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521; wenbo.ma@ucr.edu majb@fudan.edu.cn.,Department of Chemistry , University of Connecticut , 55 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.,Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA.,Structural Genomics Consortium , Johann Wolfgang Goethe University , Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15 , D-60438 Frankfurt am Main , DE , Germany.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Biotechnology Research Division , Korea Atomic Energy Research Institute (KAERI) , Jeongeup 56212 , Republic of Korea.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. charles.sindelar@yale.edu.,c Institut de Biologie Physico-Chimique , IBPC, CNRS , Paris , France.,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe University , Max-von-Laue-Str. 9 , D-60438 Frankfurt am Main , DE , Germany.,Department of Plant Pathology, Nanjing Agriculture University, 210095 Nanjing, China.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: jrmarszalek@mdanderson.org.,Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: patrick@salk.edu.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016.,Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287.,Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN 46202, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Department of Chemistry & Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea.,Department of Food Science and Engineering , Ewha Womans University , Seoul 03760 , Republic of Korea.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.,Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Biology, Indiana University, Bloomington, IN 47405 cedann@indiana.edu dbkearns@indiana.edu.,Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Pharmacy , Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany.,Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Leicester Tuberculosis Research Group (LTBRG) and Leicester Institute of Structural and Chemical Biology (LISCB), Department of Respiratory Science & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Institute of Molecular and Cell Biology, Singapore 138673.,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.,Department of Molecular and Cellular Biology , University of Connecticut , 91 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, 6997801, Israel.,Institut de Biologie Structurale, Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Grenoble, 38044, France.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States.,Department of Pharmacology, Yale University, New Haven, CT, USA. david.calderwood@yale.edu.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111; philim01@nyulangone.org Jinhua.wu@fccc.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016; philim01@nyulangone.org Jinhua.wu@fccc.edu.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: bracher@biochem.mpg.de.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103; thomas.pollard@yale.edu.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea. jylee001@dongguk.edu.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea. Electronic address: hscho8@yonsei.ac.kr.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. ktakeda@kuchem.kyoto-u.ac.jp.,Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre, 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada.,Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA.,Department of Microbiology, Monash University, Clayton, Australia.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.,Department of Physics, Arizona State University, Tempe, AZ 85287.,d Laboratoire de Cristallographie et RMN biologiques , CNRS, Université Paris Descartes , Paris , France.,5Department of Integrative Medical Biology (IMB), Umeå University, SE-90187 Umeå, Sweden.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,Center for Plant Cell Biology, University of California, Riverside, CA 92521.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. nyan@princeton.edu.,Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,e Laboratoire de Microbiologie , Université libre de Bruxelles (ULB) , Gosselies , Belgium.,From the Departments of Chemistry.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China. Electronic address: lugw@scu.edu.cn.,CBH, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea. Electronic address: hanc210@snu.ac.kr.,Department of Cell Biology, Yale University, New Haven, CT 06520-8103.,4Umeå Centre for Molecular Medicine (UCMM), Umeå University, SE-90187 Umeå, Sweden.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103.,Department of Molecular Biosciences, University of Kansas, Lawrence, United States.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.,Biochemistry Graduate Program, Indiana University, Bloomington, IN 47405.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.,1Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90187 Umeå, Sweden.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,2Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.,SLAC National Accelerator Laboratory, Menlo Park, CA 94025.,College of Pharmacy and Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea.,Department of Chemistry, Indiana University, Bloomington, IN 47405.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521.,Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.,State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200438 Shanghai, China.,Hauptman-Woodward Institute and SUNY University of Buffalo, Buffalo, NY 14203.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , DE , Germany.,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom.,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China; Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain.,University of Science and Technology , Daejeon , Republic of Korea.,Medicine, Vanderbilt University Medical Center, United States.,the Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, Washington 98195.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H
A
142Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 1 
Gene Names: rnhA
EC: 3.1.26.4
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KEI9
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'B4synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(P*CP*G)-3' portion of cleaved RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')b2synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')C6synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
RB
Query on RB

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Download CCD File 
A, B, C
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.856α = 90.00
b = 37.521β = 97.31
c = 62.706γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-06-09 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Samara, N.L., Yang, W.

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release