6JQ6

Hatchet Ribozyme Structure soaking with Ir(NH3)6+

  • Classification: RNA
  • Organism(s): synthetic construct

  • 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: 2.626 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

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.USA 116: 10783-10791

  • DOI: 10.1073/pnas.1902413116
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.,Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065.,Institute of Organic Chemistry, Leopold Franzens University, 6020 Innsbruck, Austria; pateld@mskcc.org ronald.micura@uibk.ac.at aimingren@zju.edu.cn.,Life Science Institute, Zhejiang University, 310058 Hangzhou, China.,Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065; pateld@mskcc.org ronald.micura@uibk.ac.at aimingren@zju.edu.cn.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.,Institute of Organic Chemistry, Leopold Franzens University, 6020 Innsbruck, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (81-MER)U81synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IRI
Query on IRI

Download SDF File 
Download CCD File 
U
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.626 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.830α = 90.00
b = 91.830β = 90.00
c = 140.627γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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)China91640104

Revision History 

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