2WJV

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unusual Bipartite Mode of Interaction between the Nonsense-Mediated Decay Factors, Upf1 and Upf2.

Clerici, M.Mourao, A.Gutsche, I.Gehring, N.H.Hentze, M.W.Kulozik, A.Kadlec, J.Sattler, M.Cusack, S.

(2009) EMBO J 28: 2293

  • DOI: 10.1038/emboj.2009.175
  • Primary Citation of Related Structures:  
    2WJV, 2WJY

  • PubMed Abstract: 
  • Nonsense-mediated decay (NMD) is a eukaryotic quality control mechanism that degrades mRNAs carrying premature stop codons. In mammalian cells, NMD is triggered when UPF2 bound to UPF3 on a downstream exon junction complex interacts with UPF1 bound t ...

    Nonsense-mediated decay (NMD) is a eukaryotic quality control mechanism that degrades mRNAs carrying premature stop codons. In mammalian cells, NMD is triggered when UPF2 bound to UPF3 on a downstream exon junction complex interacts with UPF1 bound to a stalled ribosome. We report structural studies on the interaction between the C-terminal region of UPF2 and intact UPF1. Crystal structures, confirmed by EM and SAXS, show that the UPF1 CH-domain is docked onto its helicase domain in a fixed configuration. The C-terminal region of UPF2 is natively unfolded but binds through separated alpha-helical and beta-hairpin elements to the UPF1 CH-domain. The alpha-helical region binds sixfold more weakly than the beta-hairpin, whereas the combined elements bind 80-fold more tightly. Cellular assays show that NMD is severely affected by mutations disrupting the beta-hairpin binding, but not by those only affecting alpha-helix binding. We propose that the bipartite mode of UPF2 binding to UPF1 brings the ribosome and the EJC in close proximity by forming a tight complex after an initial weak encounter with either element.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble Cedex 9, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
REGULATOR OF NONSENSE TRANSCRIPTS 1AB800Homo sapiensMutation(s): 0 
Gene Names: UPF1KIAA0221RENT1
EC: 3.6.1 (PDB Primary Data), 3.6.4 (UniProt)
Find proteins for Q92900 (Homo sapiens)
Explore Q92900 
Go to UniProtKB:  Q92900
NIH Common Fund Data Resources
PHAROS  Q92900
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
REGULATOR OF NONSENSE TRANSCRIPTS 2DE97Homo sapiensMutation(s): 0 
Gene Names: UPF2KIAA1408RENT2
Find proteins for Q9HAU5 (Homo sapiens)
Explore Q9HAU5 
Go to UniProtKB:  Q9HAU5
NIH Common Fund Data Resources
PHAROS  Q9HAU5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.41α = 90
b = 97.29β = 102.38
c = 124.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance