1UW4

The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The Structural Basis for the Interaction between Nonsense-Mediated Mrna Decay Factors Upf2 and Upf3

Kadlec, J., Izaurralde, E., Cusack, S.

(2004) Nat Struct Mol Biol 11: 330

  • DOI: 10.1038/nsmb741
  • Primary Citation of Related Structures:  
    1UW4

  • PubMed Abstract: 

    • Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in or ...

    Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast to human. We present a crystal structure at a resolution of 1.95 A of the complex between the interacting domains of human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain). The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b RNP domain, which is generally used by these domains to bind nucleic acids. We show that the UPF3b RNP does not bind RNA, whereas the UPF2 construct and the complex do. Our results advance understanding of the molecular mechanisms underlying the NMD quality control process.

    Organizational Affiliation: 

    European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UPF3XA, C91Homo sapiensMutation(s): 0 
Gene Names: UPF3B, RENT3B, UPF3X
Find proteins for Q9BZI7 (Homo sapiens)
Explore Q9BZI7 
Go to UniProtKB:  Q9BZI7
NIH Common Fund Data Resources
PHAROS  Q9BZI7
GTEx  ENSG00000125351
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 2B, D248Homo sapiensMutation(s): 0 
Gene Names: UPF2, KIAA1408, RENT2
Find proteins for Q9HAU5 (Homo sapiens)
Explore Q9HAU5 
Go to UniProtKB:  Q9HAU5
NIH Common Fund Data Resources
PHAROS  Q9HAU5
GTEx  ENSG00000151461
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME
Download Ideal Coordinates CCD File 
B, D
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.306α = 90
b = 100.178β = 90
c = 153.458γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SOLVE/RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance