4XR7

Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The structure of the Pan2-Pan3 core complex reveals cross-talk between deadenylase and pseudokinase.

Schafer, I.B.Rode, M.Bonneau, F.Schussler, S.Conti, E.

(2014) Nat Struct Mol Biol 21: 591-598

  • DOI: https://doi.org/10.1038/nsmb.2834
  • Primary Citation of Related Structures:  
    4Q8G, 4Q8H, 4XR7

  • PubMed Abstract: 

    Pan2-Pan3 is a conserved complex involved in the shortening of mRNA poly(A) tails, the initial step in eukaryotic mRNA turnover. We show that recombinant Saccharomyces cerevisiae Pan2-Pan3 can deadenylate RNAs in vitro without needing the poly(A)-binding protein Pab1. The crystal structure of an active ~200-kDa core complex reveals that Pan2 and Pan3 interact with an unusual 1:2 stoichiometry imparted by the asymmetric nature of the Pan3 homodimer. An extended region of Pan2 wraps around Pan3 and provides a major anchoring point for complex assembly. A Pan2 module formed by the pseudoubiquitin-hydrolase and RNase domains latches onto the Pan3 pseudokinase with intertwined interactions that orient the deadenylase active site toward the A-binding site of the interacting Pan3. The molecular architecture of Pan2-Pan3 suggests how the nuclease and its pseudokinase regulator act in synergy to promote deadenylation.


  • Organizational Affiliation

    Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PAB-dependent poly(A)-specific ribonuclease subunit PAN2A [auth G],
F [auth D],
I [auth J],
L [auth A]
776Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PAN2YGL094C
EC: 3.1.13.4
UniProt
Find proteins for P53010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53010 
Go to UniProtKB:  P53010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53010
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PAB-dependent poly(A)-specific ribonuclease subunit PAN3465Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PAN3ECM35YKL025C
UniProt
Find proteins for P36102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36102 
Go to UniProtKB:  P36102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36102
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.443α = 90
b = 205.298β = 94.1
c = 234.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany294371
DFGGermanySFB646
DFGGermanySFB1035
DFGGermanyGRK1721
DFGGermanyFOR1680
DFGGermanyCIPSM

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release