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 

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

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymyositis/scleroderma autoantigen 1
A
358Homo sapiensGene Names: EXOSC9 (PMSCL1)
Find proteins for Q06265 (Homo sapiens)
Go to Gene View: EXOSC9
Go to UniProtKB:  Q06265
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP41
B
249Homo sapiensGene Names: EXOSC4 (RRP41, SKI6)
Find proteins for Q9NPD3 (Homo sapiens)
Go to Gene View: EXOSC4
Go to UniProtKB:  Q9NPD3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP43
C
278Homo sapiensGene Names: EXOSC8 (OIP2, RRP43)
Find proteins for Q96B26 (Homo sapiens)
Go to Gene View: EXOSC8
Go to UniProtKB:  Q96B26
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP46
D
237Homo sapiensGene Names: EXOSC5 (CML28, RRP46)
Find proteins for Q9NQT4 (Homo sapiens)
Go to Gene View: EXOSC5
Go to UniProtKB:  Q9NQT4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP42
E
305Homo sapiensGene Names: EXOSC7 (KIAA0116, RRP42)
Find proteins for Q15024 (Homo sapiens)
Go to Gene View: EXOSC7
Go to UniProtKB:  Q15024
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome component 6
F
272Homo sapiensGene Names: EXOSC6 (MTR3)
Find proteins for Q5RKV6 (Homo sapiens)
Go to Gene View: EXOSC6
Go to UniProtKB:  Q5RKV6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP40
G
289Homo sapiensGene Names: EXOSC3 (RRP40)
Find proteins for Q9NQT5 (Homo sapiens)
Go to Gene View: EXOSC3
Go to UniProtKB:  Q9NQT5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP4
H
308Homo sapiensGene Names: EXOSC2 (RRP4)
Find proteins for Q13868 (Homo sapiens)
Go to Gene View: EXOSC2
Go to UniProtKB:  Q13868
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
3'-5' exoribonuclease CSL4 homolog
I
209Homo sapiensGene Names: EXOSC1 (CSL4)
Find proteins for Q9Y3B2 (Homo sapiens)
Go to Gene View: EXOSC1
Go to UniProtKB:  Q9Y3B2
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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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 
  • Space Group: P 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 307.800α = 90.00
b = 307.800β = 90.00
c = 307.800γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
DENZOdata reduction
MLPHAREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance