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 

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This is version 1.2 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 28: 825

  • 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 initiation inhibition ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IA389Mus musculusMutation(s): 0 
Gene Names: Eif4a1Ddx2aEif4a
EC: 3.6.4.13
UniProt
Find proteins for P60843 (Mus musculus)
Explore P60843 
Go to UniProtKB:  P60843
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')B10synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V6D (Subject of Investigation/LOI)
Query on V6D

Download Ideal Coordinates CCD File 
E [auth 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 (Subject of Investigation/LOI)
Query on ANP

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

Download Ideal Coordinates CCD File 
D [auth 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

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references