2XZL

Upf1-RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2.

Chakrabarti, S.Jayachandran, U.Bonneau, F.Fiorini, F.Basquin, C.Domcke, S.Le Hir, H.Conti, E.

(2011) Mol Cell 41: 693

  • DOI: 10.1016/j.molcel.2011.02.010
  • Primary Citation of Related Structures:  
    2XZL, 2XZO, 2XZP

  • PubMed Abstract: 
  • Upf1 is a crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons. The essential RNA-dependent ATPase activity of Upf1 is triggered by the formation of the surveillance complex with Upf2-Upf3 ...

    Upf1 is a crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons. The essential RNA-dependent ATPase activity of Upf1 is triggered by the formation of the surveillance complex with Upf2-Upf3. We report crystal structures of Upf1 in the presence and absence of the CH domain, captured in the transition state with ADP:AlF₄⁻ and RNA. In isolation, Upf1 clamps onto the RNA, enclosing it in a channel formed by both the catalytic and regulatory domains. Upon binding to Upf2, the regulatory CH domain of Upf1 undergoes a large conformational change, causing the catalytic helicase domain to bind RNA less extensively and triggering its helicase activity. Formation of the surveillance complex thus modifies the RNA binding properties and the catalytic activity of Upf1, causing it to switch from an RNA-clamping mode to an RNA-unwinding mode.


    Organizational Affiliation

    Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, D-82152 Martinsried, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT HELICASE NAM7A802Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13 (PDB Primary Data), 3.6.4 (UniProt)
Find proteins for P30771 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30771 
Go to UniProtKB:  P30771
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3B9synthetic construct
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    F [auth A]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    1PE
    Query on 1PE

    Download Ideal Coordinates CCD File 
    I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , O [auth A] , P [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]
    PENTAETHYLENE GLYCOL
    C10 H22 O6
    JLFNLZLINWHATN-UHFFFAOYSA-N
     Ligand Interaction
    ALF
    Query on ALF

    Download Ideal Coordinates CCD File 
    G [auth A]TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A], E [auth A]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    H [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.40 Å
    • R-Value Free: 0.243 
    • R-Value Work: 0.197 
    • R-Value Observed: 0.200 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 64.135α = 90
    b = 114.117β = 110.24
    c = 65.73γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2011-03-30
      Type: Initial release