5Y87

Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme

Zheng, L.Mairhofer, E.Teplova, M.Zhang, Y.Ma, J.Patel, D.J.Micura, R.Ren, A.

(2017) Nat Commun 8: 1180-1180

  • DOI: 10.1038/s41467-017-01276-y
  • Primary Citation of Related Structures:  
    5Y85, 5Y87

  • PubMed Abstract: 
  • Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg 2+ cations ...

    Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg 2+ cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg 2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.


    Organizational Affiliation

    Collaborative Innovation Centre of Genetics and Development, Fudan University, 200438, Shanghai, China. AimingRen@zju.edu.cn.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')A, C18metagenome
    Find similar nucleic acids by: Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA/RNA (50-MER)B, D50metagenome
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    E [auth A] , F [auth A] , G [auth B] , H [auth B] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , 
    E [auth A],  F [auth A],  G [auth B],  H [auth B],  I [auth B],  J [auth B],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth C],  S [auth D],  T [auth D],  U [auth D],  V [auth D],  W [auth D],  X [auth D],  Y [auth D],  Z [auth D]
    MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.13 Å
    • R-Value Free: 0.257 
    • R-Value Work: 0.202 
    • R-Value Observed: 0.205 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 91.221α = 90
    b = 108.963β = 90
    c = 41.794γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2017-11-22
      Type: Initial release
    • Version 2.0: 2019-01-23
      Changes: Atomic model, Data collection, Derived calculations