2GK6

Structural and Functional insights into the human Upf1 helicase core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
ADSCdata collection
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



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