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 1.2 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: 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 fr ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Polymyositis/scleroderma autoantigen 1 A358Homo sapiensMutation(s): 0 
Gene Names: PMSCL1, EXOSC9
Find proteins for Q06265 (Homo sapiens)
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PHAROS:  Q06265
GTEx:  ENSG00000123737
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP41 B249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4, RRP41, SKI6
EC: 3.1.13
Find proteins for Q9NPD3 (Homo sapiens)
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PHAROS:  Q9NPD3
GTEx:  ENSG00000178896
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP43 C278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8, OIP2, RRP43
EC: 3.1.13
Find proteins for Q96B26 (Homo sapiens)
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PHAROS:  Q96B26
GTEx:  ENSG00000120699
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP46 D237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5, CML28, RRP46
EC: 3.1.13
Find proteins for Q9NQT4 (Homo sapiens)
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PHAROS:  Q9NQT4
GTEx:  ENSG00000077348
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP42 E305Homo sapiensMutation(s): 1 
Gene Names: EXOSC7, KIAA0116, RRP42
EC: 3.1.13
Find proteins for Q15024 (Homo sapiens)
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PHAROS:  Q15024
GTEx:  ENSG00000075914
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome component 6 F272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6, MTR3
Find proteins for Q5RKV6 (Homo sapiens)
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PHAROS:  Q5RKV6
GTEx:  ENSG00000223496
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP40 G289Homo sapiensMutation(s): 0 
Gene Names: EXOSC3, RRP40, CGI-102
EC: 3.1.13
Find proteins for Q9NQT5 (Homo sapiens)
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PHAROS:  Q9NQT5
GTEx:  ENSG00000107371
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP4 H308Homo sapiensMutation(s): 0 
Gene Names: EXOSC2, RRP4
EC: 3.1.13
Find proteins for Q13868 (Homo sapiens)
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PHAROS:  Q13868
GTEx:  ENSG00000130713
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
3'-5' exoribonuclease CSL4 homolog I209Homo sapiensMutation(s): 0 
Gene Names: EXOSC1, CSL4, CGI-108
EC: 3.1.13
Find proteins for Q9Y3B2 (Homo sapiens)
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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

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Entry History 

Deposition Data

  • Deposited Date: 2006-10-23 
  • Released Date: 2006-12-26 
    • Deposition Author(s): Lima, C.D.

Revision History 

  • 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