Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 225184.78 
• Atom Count: 14232 
• Residue Count: 1948 
• Unique protein chains: 2

4I43

Crystal structure of Prp8:Aar2 complex

• DOI: 10.2210/pdb4I43/pdb

• Classification: SPLICING
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Saccharomyces cerevisiae


• Deposited: 2012-11-27 Released: 2013-01-23 
• Deposition Author(s): Galej, W.P., Oubridge, C., Newman, A.J., Nagai, K.

---

Experimental Data Snapshot

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

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

• PubMed: 23354046 
• DOI: 10.1038/nature11843
• Primary Citation of Related Structures:  
  3ZEF


• 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 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 II 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 II 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
Molecule	Chains	Sequence Length	Organism	Details
A1 cistron-splicing factor AAR2	A	384	Saccharomyces 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
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing factor 8	B	1564	Saccharomyces 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 = 118.856	α = 90.00
b = 158.595	β = 90.00
c = 220.507	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
MOLREP	phasing
Aimless	data scaling
MxCuBE	data collection
PHASER	phasing
SHELXE	model building
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-27 
• Released Date: 2013-01-23 
• Deposition Author(s): Galej, W.P., Oubridge, C., Newman, A.J., Nagai, K.

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