6CHR

Crystal structure of a group II intron lariat with an intact 3' splice site (pre-2s state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the second step of group II intron splicing.

Chan, R.T.Peters, J.K.Robart, A.R.Wiryaman, T.Rajashankar, K.R.Toor, N.

(2018) Nat Commun 9: 4676-4676

  • DOI: 10.1038/s41467-018-06678-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related. Here we report the 3.7 Å crystal structure of a eukaryotic group II intron in the lariat-3' exon form, immediately preceding ...

    The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related. Here we report the 3.7 Å crystal structure of a eukaryotic group II intron in the lariat-3' exon form, immediately preceding the second step of splicing, analogous to the spliceosomal P complex. This structure reveals the location of the intact 3' splice site within the catalytic core of the group II intron. The 3'-OH of the 5' exon is positioned in close proximity to the 3' splice site for nucleophilic attack and exon ligation. The active site undergoes conformational rearrangements with the catalytic triplex having different configurations before and after the second step of splicing. We describe a complete model for the second step of group II intron splicing that incorporates a dynamic catalytic triplex being responsible for creating the binding pocket for 3' splice site capture.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (621-MER)A625Pylaiella littoralis
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3')B13Pylaiella littoralis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 165.015α = 90.00
b = 256.893β = 90.00
c = 137.232γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXDEphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5R01GM102216
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM123275
National Institutes of Health/National Institute of General Medical SciencesUnited States5P41GM103403
National Institutes of Health/National Institute of General Medical SciencesUnited States5T32GM007240
National Institutes of Health/National Institute of General Medical SciencesUnited States5T32GM008326

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release