Structural and Functional insights into the human Upf1 helicase core

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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Structural and functional insights into the human Upf1 helicase core

Cheng, Z.Muhlrad, D.Lim, M.K.Parker, R.Song, H.

(2007) EMBO J 26: 253-264

  • DOI: https://doi.org/10.1038/sj.emboj.7601464
  • Primary Citation of Related Structures:  
    2GJK, 2GK6, 2GK7

  • PubMed Abstract: 

    Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway that recognizes and degrades aberrant mRNAs containing premature stop codons. A critical protein in NMD is Upf1p, which belongs to the helicase super family 1 (SF1), and is thought to utilize the energy of ATP hydrolysis to promote transitions in the structure of RNA or RNA-protein complexes. The crystal structure of the catalytic core of human Upf1p determined in three states (phosphate-, AMPPNP- and ADP-bound forms) reveals an overall structure containing two RecA-like domains with two additional domains protruding from the N-terminal RecA-like domain. Structural comparison combined with mutational analysis identifies a likely single-stranded RNA (ssRNA)-binding channel, and a cycle of conformational change coupled to ATP binding and hydrolysis. These conformational changes alter the likely ssRNA-binding channel in a manner that can explain how ATP binding destabilizes ssRNA binding to Upf1p.

  • Organizational Affiliation

    Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, Singapore, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of nonsense transcripts 1
A, B
624Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92900 (Homo sapiens)
Explore Q92900 
Go to UniProtKB:  Q92900
GTEx:  ENSG00000005007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92900
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.284α = 114.41
b = 67.836β = 90.13
c = 87.25γ = 110.22
Software Package:
Software NamePurpose
ADSCdata collection
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description