4MS9

Native RNA-10mer Structure: ccggcgccgg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the effects of 2'-5' linkages on the RNA duplex.

Sheng, J.Li, L.Engelhart, A.E.Gan, J.Wang, J.Szostak, J.W.

(2014) Proc Natl Acad Sci U S A 111: 3050-3055

  • DOI: 10.1073/pnas.1317799111
  • Primary Citation of Related Structures:  
    4MS9, 4MSR, 4MSB

  • PubMed Abstract: 
  • The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity ...

    The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2'-5' linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.


    Organizational Affiliation

    Howard Hughes Medical Institute and Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, Boston, MA 02114.



Macromolecules
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    Native RNA duplex 10merA10N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SR
    Query on SR

    Download Ideal Coordinates CCD File 
    B [auth A], C [auth A], D [auth A]STRONTIUM ION
    Sr
    PWYYWQHXAPXYMF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.32 Å
    • R-Value Free: 0.228 
    • R-Value Work: 0.188 
    • R-Value Observed: 0.190 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 22.708α = 90
    b = 22.708β = 90
    c = 77.721γ = 120
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    ACORNphasing
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-02-12
      Type: Initial release
    • Version 1.1: 2014-03-19
      Changes: Database references
    • Version 1.2: 2018-01-24
      Changes: Structure summary
    • Version 1.3: 2020-02-26
      Changes: Data collection