6C8D

RNA-dGMP complex with Mg ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic observation of nonenzymatic RNA primer extension.

Zhang, W.Walton, T.Li, L.Szostak, J.W.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.36422
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of lif ...

    The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process.


    Organizational Affiliation

    College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shanxi, China.,College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305; shannon-au@cuhk.edu.hk wahc@stanford.edu.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland thilo.kohler@unige.ch.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Biological Science Imaging facility (BSIR), Department of Biology, 89 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA.,Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: titoh@ac.shoyaku.ac.jp.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.,NAmur MEdicine & Drug Innovation Center (NAMEDIC), NARILIS, UNamur , rue de Bruxelles 61 , B-5000 Namur , Belgium.,Institute of Chemical Biology and Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. becker@genzentrum.lmu.de.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812.,School of Biological Sciences, Nanyang Technological University, Singapore 637551; ygao@ntu.edu.sg yangliang@ntu.edu.sg rero@ntu.edu.sg.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beatrix@genzentrum.lmu.de.,College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA hughesst@mail.nih.gov.,Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.,Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM) , ULiège , Quartier Hôpital, Avenue Hippocrate, 15, B36 , B-4000 Liège , Belgium.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.,CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA.,Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark.,Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA e-filippova@northwestern.edu wf-anderson@northwestern.edu.,Jacobs University, Bremen, Germany.,Rega Institute for Medical Research and Department of Microbiology and Immunology, Leuven, Belgium.,Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases , ULiège , B34, Quartier Hôpital, Avenue de l'hôpital, 11 , B-4000 Liège , Belgium.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: tgonen@ucla.edu.,School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China.,Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong.,Biozentrum, University of Basel, Basel, Switzerland.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong; shannon-au@cuhk.edu.hk wahc@stanford.edu.,School of Biological Sciences, Nanyang Technological University, Singapore 637551.,Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.,Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 6767 Bertner Avenue, Houston, TX 77225, USA.,Institute of Structural Biology, Nanyang Technological University, Singapore 639798.,National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA.,Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800 VIC, Australia. Electronic address: fionna.loughlin@monash.edu.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA. Electronic address: jsuh@rice.edu.,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,GE Healthcare Life Sciences, Beijing 100176, China.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673.,College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shanxi, China; College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China. Electronic address: zhanggaiping2003@163.com.,Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA.,Keck Biophysics Facility, Northwestern University, Evanston, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')A,B14synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DG
Query on DG

Download SDF File 
Download CCD File 
A, B
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LCG
Query on LCG
A, B
RNA LINKINGC11 H14 N5 O8 PDG
LCC
Query on LCC
A, B
RNA LINKINGC11 H16 N3 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.547α = 90.00
b = 49.547β = 90.00
c = 81.337γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references