2WJV

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

• PDB DOI:  https://doi.org/10.2210/pdb2WJV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-06-01 Released: 2009-07-07 
• Deposition Author(s): Clerici, M., Mourao, A., Gutsche, I., Gehring, N.H., Hentze, M.W., Kulozik, A., Kadlec, J., Sattler, M., Cusack, S.

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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 

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

• PubMed: 19556969 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 203.85 kDa 
• Atom Count: 13,187 
• Modelled Residue Count: 1,654 
• Deposited Residue Count: 1,794 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATOR OF NONSENSE TRANSCRIPTS 1	A, B	800	Homo sapiens	Mutation(s): 0  Gene Names: UPF1, KIAA0221, RENT1 EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92900 (Homo sapiens) Explore Q92900  Go to UniProtKB:  Q92900
PHAROS:  Q92900

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATOR OF NONSENSE TRANSCRIPTS 2	C [auth D], D [auth E]	97	Homo sapiens	Mutation(s): 0  Gene Names: UPF2, KIAA1408, RENT2
UniProt
Find proteins for Q9HAU5 (Homo sapiens) Explore Q9HAU5  Go to UniProtKB:  Q9HAU5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A], G [auth A], U [auth B], V [auth B], W [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 92.41	α = 90
b = 97.29	β = 102.38
c = 124.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Clerici, M., Mourao, A., Gutsche, I., Gehring, N.H., Hentze, M.W., Kulozik, A., Kadlec, J., Sattler, M., Cusack, S.

Revision History  

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