3M7N

archaeoglobus fulgidus exosome with RNA bound to the active site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Quantitative analysis of processive RNA degradation by the archaeal RNA exosome

Hartung, S., Niederberger, T., Hartung, M., Tresch, A., Hopfner, K.-P.

(2010) Nucleic Acids Res. 38: 5166-5176

  • DOI: 10.1093/nar/gkq238
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • RNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-bind ...

    RNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-binding domains. RNA degradation by RNA exosomes has not been studied in a quantitative manner because of the complex kinetics involved, and exosome features contributing to efficient RNA degradation remain unclear. Here we derive a quantitative kinetic model for degradation of a model substrate by the archaeal exosome. Markov Chain Monte Carlo methods for parameter estimation allow for the comparison of reaction kinetics between different exosome variants and substrates. We show that long substrates are degraded in a processive and short RNA in a more distributive manner and that the cap proteins influence degradation speed. Our results, supported by small angle X-ray scattering, suggest that the Rrp4-type cap efficiently recruits RNA but prevents fast RNA degradation of longer RNAs by molecular friction, likely by RNA contacts to its unique KH-domain. We also show that formation of the RNase-PH like ring with entrapped RNA is not required for high catalytic efficiency, suggesting that the exosome chamber evolved for controlled processivity, rather than for catalytic chemistry in RNA decay.

    Organizational Affiliation: 

    Center for Integrated Protein Sciences, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein AF_0206
A, B, C
179Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: csl4
Find proteins for O30033 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O30033
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable exosome complex exonuclease 1
D, E, F
258Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 1 
Gene Names: rrp41
EC: 3.1.13.-
Find proteins for O29757 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O29757
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Probable exosome complex exonuclease 2
G, H, I
259Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: rrp42
Find proteins for O29756 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O29756
Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(*C*UP*CP*CP*CP*C)-3'X,Y,Z6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 138.268α = 90.00
b = 138.268β = 90.00
c = 262.273γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DNAdata collection
PHENIXrefinement
SCALEPACKdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance