4E8R

Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Visualizing Group II Intron Catalysis through the Stages of Splicing.

Marcia, M.Pyle, A.M.

(2012) Cell 151: 497-507

  • DOI: 10.1016/j.cell.2012.09.033
  • Primary Citation of Related Structures:  4E8K, 4E8M, 4E8N, 4E8P, 4E8Q, 4E8T, 4E8V, 4FAQ, 4FAU, 4FAW, 4FAX, 4FB0, 4FAR

  • PubMed Abstract: 
  • Group II introns are self-splicing ribozymes that share a reaction mechanism and a common ancestor with the eukaryotic spliceosome, thereby providing a model system for understanding the chemistry of pre-mRNA splicing. Here we report 14 crystal struc ...

    Group II introns are self-splicing ribozymes that share a reaction mechanism and a common ancestor with the eukaryotic spliceosome, thereby providing a model system for understanding the chemistry of pre-mRNA splicing. Here we report 14 crystal structures of a group II intron at different stages of catalysis. We provide a detailed mechanism for the first step of splicing, we describe a reversible conformational change between the first and the second steps of splicing, and we present the ligand-free intron structure after splicing in an active state that corresponds to the retrotransposable form of the intron. During each reaction, the reactants are aligned and activated by a heteronuclear four-metal-ion center that contains a metal cluster and obligate monovalent cations, and they adopt a structural arrangement similar to that of protein endonucleases. Based on our data, we propose a model for the splicing cycle and show that it is applicable to the eukaryotic spliceosome.


    Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Group IIC intronA393Oceanobacillus iheyensis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CS
Query on CS

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Download CCD File 
A
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.200α = 90.00
b = 94.915β = 90.00
c = 225.710γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-20 
  • Released Date: 2012-11-14 
  • Deposition Author(s): Marcia, M., Pyle, A.M.

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release