4JKD

Open and closed forms of I1790Y human PRP8 RNase H-like domain with bound Mg ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation.

Schellenberg, M.J.Wu, T.Ritchie, D.B.Fica, S.Staley, J.P.Atta, K.A.Lapointe, P.Macmillan, A.M.

(2013) Nat.Struct.Mol.Biol. 20: 728-734

  • DOI: 10.1038/nsmb.2556
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Splicing of pre-mRNAs in eukaryotes is catalyzed by the spliceosome, a large RNA-protein metalloenzyme. The catalytic center of the spliceosome involves a structure comprising the U2 and U6 snRNAs and includes a metal bound by U6 snRNA. The precise a ...

    Splicing of pre-mRNAs in eukaryotes is catalyzed by the spliceosome, a large RNA-protein metalloenzyme. The catalytic center of the spliceosome involves a structure comprising the U2 and U6 snRNAs and includes a metal bound by U6 snRNA. The precise architecture of the splicesome active site, however, and the question of whether it includes protein components, remains unresolved. A wealth of evidence places the protein PRP8 at the heart of the spliceosome through assembly and catalysis. Here we provide evidence that the RNase H domain of PRP8 undergoes a conformational switch between the two steps of splicing, rationalizing yeast prp8 alleles that promote either the first or second step. We also show that this switch unmasks a metal-binding site involved in the second step. Together, these data establish that PRP8 is a metalloprotein that promotes exon ligation within the spliceosome.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
A, B
222Homo sapiensMutation(s): 1 
Gene Names: PRPF8 (PRPC8)
Find proteins for Q6P2Q9 (Homo sapiens)
Go to Gene View: PRPF8
Go to UniProtKB:  Q6P2Q9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.407α = 90.00
b = 77.738β = 90.00
c = 94.196γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
ADSCdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references
  • Version 1.2: 2013-06-26
    Type: Database references