2JEB

Structure of a 9-subunit archaeal exosome bound to Mn ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

RNA Channelling by the Archaeal Exosome.

Lorentzen, E.Dziembowski, A.Lindner, D.Seraphin, B.Conti, E.

(2007) Embo Rep. 8: 470

  • DOI: 10.1038/sj.embor.7400945
  • Primary Citation of Related Structures:  2JE6, 2JEA

  • PubMed Abstract: 
  • Exosomes are complexes containing 3' --> 5' exoribonucleases that have important roles in processing, decay and quality control of various RNA molecules. Archaeal exosomes consist of a hexameric core of three active RNase PH subunits (ribosomal RNA p ...

    Exosomes are complexes containing 3' --> 5' exoribonucleases that have important roles in processing, decay and quality control of various RNA molecules. Archaeal exosomes consist of a hexameric core of three active RNase PH subunits (ribosomal RNA processing factor (Rrp)41) and three inactive RNase PH subunits (Rrp42). A trimeric ring of subunits with putative RNA-binding domains (Rrp4/cep1 synthetic lethality (Csl)4) is positioned on top of the hexamer on the opposite side to the RNA degrading sites. Here, we present the 1.6 A resolution crystal structure of the nine-subunit exosome of Sulfolobus solfataricus and the 2.3 A structure of this complex bound to an RNA substrate designed to be partly trimmed rather than completely degraded. The RNA binds both at the active site on one side of the molecule and on the opposite side in the narrowest constriction of the central channel. Multiple substrate-binding sites and the entrapment of the substrate in the central channel provide a rationale for the processive degradation of extended RNAs and the stalling of structured RNAs.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany. lorentze@embl.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX EXONUCLEASE 2
A
277Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Gene Names: rrp42
Find proteins for Q9UXC0 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q9UXC0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX EXONUCLEASE 1
B
250Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Gene Names: rrp41
EC: 3.1.13.-
Find proteins for Q9UXC2 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q9UXC2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX RNA-BINDING PROTEIN 1
I
251Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Gene Names: rrp4
Find proteins for Q9UXC4 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q9UXC4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, I
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 133.640α = 90.00
b = 133.640β = 90.00
c = 133.640γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance