6XKI

Crystal structure of eIF4A-I in complex with RNA bound to des-MePateA, a pateamine A analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A.

Naineni, S.K.Liang, J.Hull, K.Cencic, R.Zhu, M.Northcote, P.Teesdale-Spittle, P.Romo, D.Nagar, B.Pelletier, J.

(2021) Cell Chem Biol 

  • DOI: 10.1016/j.chembiol.2020.12.006
  • Primary Citation of Related Structures:  
    6XKI

  • PubMed Abstract: 
  • Interfacial inhibitors exert their biological effects through co-association with two macromolecules. The pateamine A (PatA) class of molecules function by stabilizing eukaryotic initiation factor (eIF) 4A RNA helicase onto RNA, resulting in translation ...

    Interfacial inhibitors exert their biological effects through co-association with two macromolecules. The pateamine A (PatA) class of molecules function by stabilizing eukaryotic initiation factor (eIF) 4A RNA helicase onto RNA, resulting in translation initiation inhibition. Here, we present the crystal structure of an eIF4A1:RNA complex bound to an analog of the marine sponge-derived natural product PatA, C5-desmethyl PatA (DMPatA). One end of this small molecule wedges itself between two RNA bases while the other end is cradled by several protein residues. Strikingly, DMPatA interacts with the eIF4A1:RNA complex in an almost identical fashion as rocaglamide A (RocA), despite being completely unrelated from a structural standpoint. The structural data rationalize the ability of PatA analogs to target a wider range of RNA substrates compared to RocA. We define the molecular basis of how DMPatA is able to clamp eIF4A1 onto RNA, imparting potent inhibitory properties to this molecule.


    Organizational Affiliation

    McGill University, Department of Biochemistry, Rm 810, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Department of Oncology, McGill University, Montreal, Quebec, Canada; Rosalind and Morris Goodman Cancer Research Center, Montreal H3A 1A3, Canada. Electronic address: jerry.pelletier@mcgill.ca.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-I A389Mus musculusMutation(s): 0 
Gene Names: Eif4a1Ddx2aEif4a
EC: 3.6.4.13
Find proteins for P60843 (Mus musculus)
Explore P60843 
Go to UniProtKB:  P60843
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')B10synthetic construct
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    V6D
    Query on V6D

    Download Ideal Coordinates CCD File 
    A
    (3S,6Z,8E,11S,15R)-15-amino-3-[(1E,3E,5E)-7-(dimethylamino)-2,5-dimethylhepta-1,3,5-trien-1-yl]-9,11-dimethyl-4,12-dioxa-20-thia-21-azabicyclo[16.2.1]henicosa-1(21),6,8,18-tetraene-5,13-dione
    C30 H43 N3 O4 S
    OKCOLQKYUABEJR-GFYARHHKSA-N
     Ligand Interaction
    ANP
    Query on ANP

    Download Ideal Coordinates CCD File 
    A
    PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    C10 H17 N6 O12 P3
    PVKSNHVPLWYQGJ-KQYNXXCUSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.87 Å
    • R-Value Free: 0.262 
    • R-Value Work: 0.222 
    • R-Value Observed: 0.224 
    • Space Group: I 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 66.785α = 90
    b = 99.942β = 90
    c = 153.663γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Canadian Institutes of Health Research (CIHR)CanadaMOP-133535

    Revision History 

    • Version 1.0: 2021-01-06
      Type: Initial release
    • Version 1.1: 2021-01-20
      Changes: Database references