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
  • Structures With Same Primary Citation

  • 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 exosome ...

    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 LengthOrganismDetails
Polymyositis/scleroderma autoantigen 1
A
358Homo sapiensMutation(s): 0 
Gene Names: PMSCL1EXOSC9
Find proteins for Q06265 (Homo sapiens)
Go to UniProtKB:  Q06265
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PHAROS  Q06265

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP43
C
278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8OIP2RRP43
EC: 3.1.13
Find proteins for Q96B26 (Homo sapiens)
Go to UniProtKB:  Q96B26
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PHAROS  Q96B26

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP46
D
237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5CML28RRP46
EC: 3.1.13
Find proteins for Q9NQT4 (Homo sapiens)
Go to UniProtKB:  Q9NQT4
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PHAROS  Q9NQT4

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP42
E
305Homo sapiensMutation(s): 1 
Gene Names: EXOSC7KIAA0116RRP42
EC: 3.1.13
Find proteins for Q15024 (Homo sapiens)
Go to UniProtKB:  Q15024
NIH Common Fund Data Resources
PHAROS  Q15024

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome component 6
F
272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6MTR3
Find proteins for Q5RKV6 (Homo sapiens)
Go to UniProtKB:  Q5RKV6
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PHAROS  Q5RKV6

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP40
G
289Homo sapiensMutation(s): 0 
Gene Names: EXOSC3RRP40CGI-102
EC: 3.1.13
Find proteins for Q9NQT5 (Homo sapiens)
Go to UniProtKB:  Q9NQT5
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PHAROS  Q9NQT5

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP4
H
308Homo sapiensMutation(s): 0 
Gene Names: EXOSC2RRP4
EC: 3.1.13
Find proteins for Q13868 (Homo sapiens)
Go to UniProtKB:  Q13868
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PHAROS  Q13868

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
3'-5' exoribonuclease CSL4 homolog
I
209Homo sapiensMutation(s): 0 
Gene Names: EXOSC1CSL4CGI-108
EC: 3.1.13
Find proteins for Q9Y3B2 (Homo sapiens)
Go to UniProtKB:  Q9Y3B2
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PHAROS  Q9Y3B2

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP41
B
249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4RRP41SKI6
EC: 3.1.13
Find proteins for Q9NPD3 (Homo sapiens)
Go to UniProtKB:  Q9NPD3
NIH Common Fund Data Resources
PHAROS  Q9NPD3
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

  • 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