Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 36.82 kDa 
• Atom Count: 2458 
• Residue Count: 310 
• Unique protein chains: 1

2IYK

Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1

• DOI: 10.2210/pdb2IYK/pdb

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


• Deposited: 2006-07-18 Released: 2006-08-30 
• Deposition Author(s): Kadlec, J., Guilligay, D., Ravelli, R.B., Cusack, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Crystal Structure of the Upf2-Interacting Domain of Nonsense-Mediated Mrna Decay Factor Upf1.

Kadlec, J., Guilligay, D., Ravelli, R.B., Cusack, S.

(2006) RNA 12: 1817

• PubMed: 16931876 
• DOI: 10.1261/rna.177606
• Primary Citation of Related Structures:  
  2IYK


• PubMed Abstract: 
  

UPF1 is an essential eukaryotic RNA helicase that plays a key role in various mRNA degradation pathways, notably nonsense-mediated mRNA decay (NMD). In combination with UPF2 and UPF3, it forms part of the surveillance complex that detects mRNAs containing premature stop codons and triggers their degradation in all organisms studied from yeast to human. We describe the 3 A resolution crystal structure of the highly conserved cysteine-histidine-rich domain of human UPF1 and show that it is a unique combination of three zinc-binding motifs arranged into two tandem modules related to the RING-box and U-box domains of ubiquitin ligases. This UPF1 domain interacts with UPF2, and we identified by mutational analysis residues in two distinct conserved surface regions of UPF1 that mediate this interaction. UPF1 residues we identify as important for the interaction with UPF2 are not conserved in UPF1 homologs from certain unicellular parasites that also appear to lack UPF2 in their genomes.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble Cedex 9, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATOR OF NONSENSE TRANSCRIPTS 1	A, B	162	Homo sapiens	Mutation(s): 0  Gene Names: UPF1, KIAA0221, RENT1 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 GTEx:  ENSG00000005007

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.56	α = 90
b = 72.98	β = 90
c = 73.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
SHARP	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-18 
• Released Date: 2006-08-30 
Deposition Author(s): Kadlec, J., Guilligay, D., Ravelli, R.B., Cusack, S.

Revision History 

• Version 1.0: 2006-08-30
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance