Hatchet Ribozyme Structure soaking with Ir(NH3)6+

  • 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

  • Resolution: 2.63 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report

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

  • 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. 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.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (81-MER)A [auth U]81synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IRI

Download Ideal Coordinates CCD File 
H18 Ir N6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.63 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.83α = 90
b = 91.83β = 90
c = 140.627γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China91640104

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references