2C38

RNase PH core of the archaeal exosome in complex with A5 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.

Lorentzen, E.Conti, E.

(2005) Mol.Cell 20: 473

  • DOI: 10.1016/j.molcel.2005.10.020
  • Primary Citation of Related Structures:  2C37, 2C39

  • PubMed Abstract: 
  • The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short ...

    The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.


    Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
A, C, E, G, I, K, M, O, Q, S, U, W
275Sulfolobus 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
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
B, D, F, H, J, L, N, P, R, T, V, X
248Sulfolobus 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, D, F, H, J, L, N, P, R, T, V, X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
B, F, H, J, N, V, X
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.276 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 206.260α = 90.00
b = 213.610β = 90.00
c = 434.040γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-23
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance