8TH6

Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity.

Yang, Z.Johnson, B.A.Meliopoulos, V.A.Ju, X.Zhang, P.Hughes, M.P.Wu, J.Koreski, K.P.Clary, J.E.Chang, T.C.Wu, G.Hixon, J.Duffner, J.Wong, K.Lemieux, R.Lokugamage, K.G.Alvarado, R.E.Crocquet-Valdes, P.A.Walker, D.H.Plante, K.S.Plante, J.A.Weaver, S.C.Kim, H.J.Meyers, R.Schultz-Cherry, S.Ding, Q.Menachery, V.D.Taylor, J.P.

(2024) Cell Rep 43: 113965-113965

  • DOI: https://doi.org/10.1016/j.celrep.2024.113965
  • Primary Citation of Related Structures:  
    8TH1, 8TH5, 8TH6, 8TH7

  • PubMed Abstract: 

    G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibits stress granule assembly and interacts with G3BP1/2 via an ITFG motif, including residue F17, in the N protein. Prior studies examining the impact of the G3PB1-N interaction on SARS-CoV-2 replication have produced inconsistent findings, and the role of this interaction in pathogenesis is unknown. Here, we use structural and biochemical analyses to define the residues required for G3BP1-N interaction and structure-guided mutagenesis to selectively disrupt this interaction. We find that N-F17A mutation causes highly specific loss of interaction with G3BP1/2. SARS-CoV-2 N-F17A fails to inhibit stress granule assembly in cells, has decreased viral replication, and causes decreased pathology in vivo. Further mechanistic studies indicate that the N-F17-mediated G3BP1-N interaction promotes infection by limiting sequestration of viral genomic RNA (gRNA) into stress granules.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, 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
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
GTEx:  ENSG00000145907 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13283
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 10
E, F, G, H
24Homo sapiensMutation(s): 0 
Gene Names: USP10KIAA0190
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14694 (Homo sapiens)
Explore Q14694 
Go to UniProtKB:  Q14694
PHAROS:  Q14694
GTEx:  ENSG00000103194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14694
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.39α = 90
b = 78.38β = 108.63
c = 73.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Structure summary