2BR2

RNase PH core of the archaeal exosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Archaeal Exosome Core is a Hexameric Ring Structure with Three Catalytic Subunits.

Lorentzen, E.Walter, P.Fribourg, S.Evguenieva-Hackenberg, E.Klug, G.Conti, E.

(2005) Nat Struct Mol Biol 12: 575

  • DOI: https://doi.org/10.1038/nsmb952
  • Primary Citation of Related Structures:  
    2BR2

  • PubMed Abstract: 

    The exosome is a 3' --> 5' exoribonuclease complex involved in RNA processing. We report the crystal structure of the RNase PH core complex of the Sulfolobus solfataricus exosome determined at a resolution of 2.8 A. The structure reveals a hexameric ring-like arrangement of three Rrp41-Rrp42 heterodimers, where both subunits adopt the RNase PH fold common to phosphorolytic exoribonucleases. Structure-guided mutagenesis reveals that the activity of the complex resides within the active sites of the Rrp41 subunits, all three of which face the same side of the hexameric structure. The Rrp42 subunit is inactive but contributes to the structuring of the Rrp41 active site. The high sequence similarity of this archaeal exosome to eukaryotic exosomes and its high structural similarity to the bacterial mRNA-degrading PNPase support a common basis for RNA-degrading machineries in all three domains of life.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EXOSOME COMPLEX EXONUCLEASE 2
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
275Saccharolobus solfataricusMutation(s): 0 
EC: 3.1.13
UniProt
Find proteins for Q9UXC0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXC0 
Go to UniProtKB:  Q9UXC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UXC0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EXOSOME COMPLEX EXONUCLEASE 1
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
248Saccharolobus solfataricusMutation(s): 0 
EC: 3.1.13
UniProt
Find proteins for Q9UXC2 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXC2 
Go to UniProtKB:  Q9UXC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UXC2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth H]
CA [auth J]
DA [auth L]
EA [auth M]
AA [auth F],
BA [auth H],
CA [auth J],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth P],
HA [auth R],
IA [auth T],
JA [auth V],
KA [auth X],
Y [auth B],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.88α = 90
b = 212.72β = 90
c = 434.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description