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



Literature

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

Naineni, S.Liang, J.Hull, K.Zhu, M.Romo, D.Nagar, B.Pelletier, J.

(2020) Cell Chem Biol 28


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IA389Mus 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