2GK7

Structural and Functional insights into the human Upf1 helicase core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/sj.emboj.7601464
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulator of nonsense transcripts 1
A
624Homo sapiensMutation(s): 0 
Gene Names: UPF1KIAA0221RENT1
EC: 3.6.1 (PDB Primary Data), 3.6.4 (UniProt)
Find proteins for Q92900 (Homo sapiens)
Go to UniProtKB:  Q92900
NIH Common Fund Data Resources
PHAROS  Q92900
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.189α = 90
b = 195.189β = 90
c = 45.458γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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