2NN6

Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Reconstitution, activities, and structure of the eukaryotic RNA exosome.

Liu, Q.Greimann, J.C.Lima, C.D.

(2006) Cell 127: 1223-1237

  • DOI: https://doi.org/10.1016/j.cell.2006.10.037
  • Primary Citation of Related Structures:  
    2NN6

  • PubMed Abstract: 

    The RNA exosome is a multisubunit 3' to 5' exoribonuclease complex that participates in degradation and processing of cellular RNA. To determine the activities and structure of the eukaryotic exosome, we report the reconstitution of 9-subunit exosomes from yeast and human and reconstitution of 10- and 11-subunit exosomes from yeast. Comparative biochemical analysis between purified subunits and reconstituted exosomes using AU-rich, polyadenylated (poly[A]), generic, and structured RNA substrates reveals processive phosphorolytic activities for human Rrp41/Rrp45 and the 9-subunit human exosome, processive hydrolytic activities for yeast Rrp44 and the yeast 10-subunit exosome, distributive hydrolytic activities for Rrp6, and processive and distributive hydrolytic activities for the yeast 11-subunit exosome. To elucidate the architecture of a eukaryotic exosome, its conserved surfaces, and the structural basis for RNA decay, we report the X-ray structure determination for the 286 kDa nine-subunit human exosome at 3.35 A.


  • Organizational Affiliation

    Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymyositis/scleroderma autoantigen 1358Homo sapiensMutation(s): 0 
Gene Names: PMSCL1
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PHAROS:  Q06265
GTEx:  ENSG00000123737 
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UniProt GroupQ06265
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP41249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4RRP41SKI6
EC: 3.1.13
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Find proteins for Q9NPD3 (Homo sapiens)
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PHAROS:  Q9NPD3
GTEx:  ENSG00000178896 
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UniProt GroupQ9NPD3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP43278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8OIP2RRP43
EC: 3.1.13
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PHAROS:  Q96B26
GTEx:  ENSG00000120699 
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UniProt GroupQ96B26
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP46237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5CML28RRP46
EC: 3.1.13
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GTEx:  ENSG00000077348 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP42305Homo sapiensMutation(s): 1 
Gene Names: EXOSC7KIAA0116RRP42
EC: 3.1.13
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GTEx:  ENSG00000075914 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome component 6272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6
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PHAROS:  Q5RKV6
GTEx:  ENSG00000223496 
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UniProt GroupQ5RKV6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP40289Homo sapiensMutation(s): 0 
Gene Names: EXOSC3RRP40
EC: 3.1.13
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PHAROS:  Q9NQT5
GTEx:  ENSG00000107371 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP4308Homo sapiensMutation(s): 0 
Gene Names: EXOSC2RRP4
EC: 3.1.13
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Find proteins for Q13868 (Homo sapiens)
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GTEx:  ENSG00000130713 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
3'-5' exoribonuclease CSL4 homolog209Homo sapiensMutation(s): 0 
Gene Names: EXOSC1CSL4
EC: 3.1.13
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Find proteins for Q9Y3B2 (Homo sapiens)
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PHAROS:  Q9Y3B2
GTEx:  ENSG00000171311 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.291 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 307.8α = 90
b = 307.8β = 90
c = 307.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2006-12-26 
  • Deposition Author(s): Lima, C.D.

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references