2WP8

yeast rrp44 nuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 

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

  • 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 ho ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP45
A
305Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP45
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT SKI6
B
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI6 (ECM20, RRP41)
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX EXONUCLEASE DIS3
J
977Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: DIS3 (RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: DIS3
Go to UniProtKB:  Q08162
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
J
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 110.900α = 90.00
b = 125.680β = 90.00
c = 139.400γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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