5ZBZ

Crystal structure of the DEAD domain of Human eIF4A with sanguinarine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling.

Jiang, C.Tang, Y.Ding, L.Tan, R.Li, X.Lu, J.Jiang, J.Cui, Z.Tang, Z.Li, W.Cao, Z.Schneider-Poetsch, T.Jiang, W.Luo, C.Ding, Y.Liu, J.Dang, Y.

(2019) Cell Chem Biol 26: 1417-1426.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2019.07.010
  • Primary Citation of Related Structures:  
    5ZBZ

  • PubMed Abstract: 

    DEAD-box ATP-dependent helicases (DEAH/D) are a family of conserved genes predominantly involved in gene expression regulation and RNA processing. As its prototype, eIF4AI is an essential component of the protein translation initiation complex. Utilizing a screening system based on wild-type eIF4AI and its L243G mutant with a changed linker domain, we discovered an eIF4AI inhibitor, sanguinarine (SAN) and used it to study the catalytic mechanism of eIF4AI. Herein, we describe the crystal structure of the eIF4AI-inhibitor complex and demonstrate that the binding site displays certain specificity, which can provide the basis for drug design to target eIF4AI. We report that except for competitive inhibition SAN's possible mechanism of action involves interference with eIF4AI catalytic cycling process by hindering the formation of the closed conformation of eIF4AI. In addition, our results highlight a new targetable site on eIF4AI and confirm eIF4AI as a viable pharmacological target.


  • Organizational Affiliation

    Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-I220Homo sapiensMutation(s): 0 
Gene Names: EIF4A1DDX2AEIF4A
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P60842 (Homo sapiens)
Explore P60842 
Go to UniProtKB:  P60842
PHAROS:  P60842
GTEx:  ENSG00000161960 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60842
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAU
Query on SAU

Download Ideal Coordinates CCD File 
B [auth A]13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium
C20 H14 N O4
INVGWHRKADIJHF-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
SAU Binding MOAD:  5ZBZ Kd: 1.25e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.471α = 90
b = 56.63β = 116.775
c = 66.324γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31470764
National Natural Science Foundation of ChinaChina21572038
National Natural Science Foundation of ChinaChina91527305

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description