5Y87

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.132 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • 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- ...

    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 Mg2+ 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 Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.


    Organizational Affiliation

    Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (50-MER)B,D50metagenome
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.132 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.221α = 90.00
b = 108.963β = 90.00
c = 41.794γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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