4I43

Crystal structure of Prp8:Aar2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Prp8 reveals active site cavity of the spliceosome.

Galej, W.P.Oubridge, C.Newman, A.J.Nagai, K.

(2013) Nature 493: 638-643

  • DOI: 10.1038/nature11843
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The active centre of the spliceosome consists of an intricate network formed by U5, U2 and U6 small nuclear RNAs, and a pre-messenger-RNA substrate. Prp8, a component of the U5 small nuclear ribonucleoprotein particle, crosslinks extensively with thi ...

    The active centre of the spliceosome consists of an intricate network formed by U5, U2 and U6 small nuclear RNAs, and a pre-messenger-RNA substrate. Prp8, a component of the U5 small nuclear ribonucleoprotein particle, crosslinks extensively with this RNA catalytic core. Here we present the crystal structure of yeast Prp8 (residues 885-2413) in complex with Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor. The structure reveals tightly associated domains of Prp8 resembling a bacterial group II intron reverse transcriptase and a type II restriction endonuclease. Suppressors of splice-site mutations, and an intron branch-point crosslink, map to a large cavity formed by the reverse transcriptase thumb, and the endonuclease-like and RNaseH-like domains. This cavity is large enough to accommodate the catalytic core of group‚ÄČII intron RNA. The structure provides crucial insights into the architecture of the spliceosome active site, and reinforces the notion that nuclear pre-mRNA splicing and group‚ÄČII intron splicing have a common origin.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A1 cistron-splicing factor AAR2
A
384Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: AAR2
Find proteins for P32357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: AAR2
Go to UniProtKB:  P32357
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
B
1564Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.856α = 90.00
b = 158.595β = 90.00
c = 220.507γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
MxCuBEdata collection
PHASERphasing
SHELXEmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary