3M7N

archaeoglobus fulgidus exosome with RNA bound to the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    3M7N, 3M85

  • 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-binding domains ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized protein AF_0206A, B, C179Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF_0206
UniProt
Find proteins for O30033 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
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Go to UniProtKB:  O30033
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UniProt GroupO30033
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Probable exosome complex exonuclease 1D, E, F258Archaeoglobus fulgidusMutation(s): 1 
Gene Names: AF_0493
EC: 3.1.13
UniProt
Find proteins for O29757 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29757 
Go to UniProtKB:  O29757
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UniProt GroupO29757
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable exosome complex exonuclease 2G, H, I259Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF_0494
EC: 3.1.13
UniProt
Find proteins for O29756 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29756 
Go to UniProtKB:  O29756
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UniProt GroupO29756
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
5'-R(*C*UP*CP*CP*CP*C)-3'J [auth X],
K [auth Y],
L [auth Z]
6N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A],
N [auth B],
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.268α = 90
b = 138.268β = 90
c = 262.273γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations