5Y85

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

  • Classification: RNA
  • Organism(s): metagenome
  • Mutation(s): No 

  • Deposited: 2017-08-18 Released: 2017-11-22 
  • Deposition Author(s): Zheng, L., Micura, R.L., Ren, A.
  • Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


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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
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AA [auth D] , BA [auth D] , CA [auth D] , DA [auth D] , E [auth A] , F [auth A] , G [auth B] , H [auth B] , 
    AA [auth D],  BA [auth D],  CA [auth D],  DA [auth D],  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 C],  T [auth D],  U [auth D],  V [auth D],  W [auth D],  X [auth D],  Y [auth D],  Z [auth D]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.237 
    • R-Value Work: 0.218 
    • R-Value Observed: 0.219 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 91.182α = 90
    b = 109.304β = 90
    c = 41.739γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of ChinaChina91640104
    National Natural Science Foundation of ChinaChina31670826

    Revision History  (Full details and data files)

    • Version 1.0: 2017-11-22
      Type: Initial release