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


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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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
PAB-dependent poly(A)-specific ribonuclease subunit PAN2L [auth A],
F [auth D],
A [auth G],
I [auth J]
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
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