8V1L

Crystal structure of the NTF2L domain of human G3BP1 in complex with small molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.395 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.281 

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Literature

Identification of small molecule inhibitors of G3BP-driven stress granule formation.

Freibaum, B.D.Messing, J.Nakamura, H.Yurtsever, U.Wu, J.Kim, H.J.Hixon, J.Lemieux, R.M.Duffner, J.Huynh, W.Wong, K.White, M.Lee, C.Meyers, R.E.Parker, R.Taylor, J.P.

(2024) J Cell Biol 223

  • DOI: https://doi.org/10.1083/jcb.202308083
  • Primary Citation of Related Structures:  
    8V1L

  • PubMed Abstract: 

    Stress granule formation is triggered by the release of mRNAs from polysomes and is promoted by the action of the RNA-binding proteins G3BP1/2. Stress granules have been implicated in several disease states, including cancer and neurodegeneration. Consequently, compounds that limit stress granule formation or promote their dissolution have potential as both experimental tools and novel therapeutics. Herein, we describe two small molecules, G3BP inhibitor a and b (G3Ia and G3Ib), designed to bind to a specific pocket in G3BP1/2 that is targeted by viral inhibitors of G3BP1/2 function. In addition to disrupting the co-condensation of RNA, G3BP1, and caprin 1 in vitro, these compounds inhibit stress granule formation in cells treated prior to or concurrent with stress and dissolve pre-existing stress granules. These effects are consistent across multiple cell types and a variety of initiating stressors. Thus, these compounds represent powerful tools to probe the biology of stress granules and hold promise for therapeutic interventions designed to modulate stress granule formation.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras GTPase-activating protein-binding protein 1
A, B, C, D, E
A, B, C, D, E, F
139Homo sapiensMutation(s): 0 
Gene Names: G3BP1G3BP
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13283 (Homo sapiens)
Explore Q13283 
Go to UniProtKB:  Q13283
PHAROS:  Q13283
GTEx:  ENSG00000145907 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13283
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.395 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.281 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.17α = 90
b = 84.69β = 91.26
c = 102.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesR35NS097974

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release