2C37

RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.266 

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:  2C38, 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RP5
Query on RP5

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Download CCD File 
N
5-O-phosphono-beta-D-ribofuranose
[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE
C5 H11 O8 P
KTVPXOYAKDPRHY-TXICZTDVSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
V
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B, D, F, H, J, L, N, P, R, T, V, X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
U5P
Query on U5P

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Download CCD File 
A, B, E, F, G, H, I, J, M, N, U, V, W, X
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.266 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 207.020α = 90.00
b = 212.940β = 90.00
c = 433.090γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction

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