6JQ5

The structure of Hatchet Ribozyme

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

  • Deposited: 2019-03-29 Released: 2019-06-12 
  • Deposition Author(s): Ren, A., Zheng, L.
  • Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Hatchet ribozyme structure and implications for cleavage mechanism.

Zheng, L.Falschlunger, C.Huang, K.Mairhofer, E.Yuan, S.Wang, J.Patel, D.J.Micura, R.Ren, A.

(2019) Proc Natl Acad Sci U S A 116: 10783-10791

  • DOI: 10.1073/pnas.1902413116
  • Primary Citation of Related Structures:  
    6JQ6, 6JQ5

  • PubMed Abstract: 
  • Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate ...

    Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5' nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.


    Organizational Affiliation

    Life Science Institute, Zhejiang University, 310058 Hangzhou, China; pateld@mskcc.org ronald.micura@uibk.ac.at aimingren@zju.edu.cn.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (82-MER)A, B82synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.582α = 90
b = 104.275β = 90
c = 126.862γ = 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

  • Deposited Date: 2019-03-29 
  • Released Date: 2019-06-12 
  • Deposition Author(s): Ren, A., Zheng, L.

Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release