2WP8

yeast rrp44 nuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation.

Bonneau, F.Basquin, J.Ebert, J.Lorentzen, E.Conti, E.

(2009) Cell 139: 547

  • DOI: 10.1016/j.cell.2009.08.042
  • Primary Citation of Related Structures:  
    2WP8

  • PubMed Abstract: 
  • The exosome is a conserved macromolecular complex essential for RNA degradation. The nine-subunit core of the eukaryotic exosome shares a similar barrel-like architecture with prokaryotic complexes, but is catalytically inert. Here, we investigate how the Rrp44 nuclease functions in the active ten-subunit exosome ...

    The exosome is a conserved macromolecular complex essential for RNA degradation. The nine-subunit core of the eukaryotic exosome shares a similar barrel-like architecture with prokaryotic complexes, but is catalytically inert. Here, we investigate how the Rrp44 nuclease functions in the active ten-subunit exosome. The 3.0 A resolution crystal structure of the yeast Rrp44-Rrp41-Rrp45 complex shows how the nuclease interacts with the exosome core and the relative accessibility of its endoribonuclease and exoribonuclease sites. Biochemical studies indicate that RNAs thread through the central channel of the core to reach the Rrp44 exoribonuclease site. This channeling mechanism involves evolutionary conserved residues. It allows the processive unwinding and degradation of RNA duplexes containing a sufficiently long single-stranded 3' extension, without the requirement for helicase activities. Although the catalytic function of the exosome core has been lost during evolution, the substrate recruitment and binding properties have been conserved from prokaryotes to eukaryotes.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT RRP45 A305Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05636 
Go to UniProtKB:  Q05636
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT SKI6 B246Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46948 
Go to UniProtKB:  P46948
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX EXONUCLEASE DIS3 J977Saccharomyces cerevisiaeMutation(s): 1 
EC: 3.1.13 (PDB Primary Data), 3.1.26 (UniProt)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08162 
Go to UniProtKB:  Q08162
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.9α = 90
b = 125.68β = 90
c = 139.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-05-30
    Changes: Other