6U8U

RNA duplex bound with TNA 3'-3' imidazolium dimer

  • Classification: RNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2019-09-05 Released: 2020-12-09 
  • Deposition Author(s): Szostak, J.W., Zhang, W.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.

Zhang, W.Kim, S.C.Tam, C.P.Lelyveld, V.S.Bala, S.Chaput, J.C.Szostak, J.W.

(2020) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkaa1215
  • Primary Citation of Related Structures:  
    6U8U, 6U8F, 6U7Y, 6U89, 6U7Z

  • PubMed Abstract: 
  • The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participa ...

    The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3'-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    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
    Q1V
    Query on Q1V

    Download Ideal Coordinates CCD File 
    A, B
    2-amino-3-[(R)-{[(3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}(hydroxy)phosphoryl]-1-[(S)-{[(3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium
    C21 H26 N13 O12 P2
    ZVPUVGSJWNSRDP-QIHYXNHISA-O
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.40 Å
    • R-Value Free: 0.267 
    • R-Value Work: 0.216 
    • R-Value Observed: 0.218 
    • Space Group: P 3 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 43.956α = 90
    b = 43.956β = 90
    c = 84.516γ = 120
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Howard Hughes Medical Institute (HHMI)United States--

    Revision History 

    • Version 1.0: 2020-12-09
      Type: Initial release
    • Version 1.1: 2021-01-06
      Changes: Database references