5DRV

Crystal structure of the G3BP2 NTF2-like domain in complex with a peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the G3BP2 NTF2-like domain in complex with a canonical FGDF motif peptide.

Kristensen, O.

(2015) Biochem.Biophys.Res.Commun. 467: 53-57

  • DOI: 10.1016/j.bbrc.2015.09.123

  • PubMed Abstract: 
  • The crystal structure of the NTF2-like domain of the human Ras GTPase SH3 Binding Protein (G3BP), isoform 2, was determined at a resolution of 2.75 Å in complex with a peptide containing a FGDF sequence motif. The overall structure of the protein is ...

    The crystal structure of the NTF2-like domain of the human Ras GTPase SH3 Binding Protein (G3BP), isoform 2, was determined at a resolution of 2.75 Å in complex with a peptide containing a FGDF sequence motif. The overall structure of the protein is highly similar to the homodimeric N-terminal domains of the G3BP1 and Rasputin proteins. Recently, a subset of G3BP interacting proteins was recognized to share a common sequence motif, FGDF. The most studied binding partners, USP10 and viral nsP3, interfere with essential G3BP functions related to assembly of cellular stress granules. Reported molecular modeling suggested that FGDF-motif containing peptides bind in an extended conformation into a hydrophobic groove on the surface of the G3BP NTF2-like domain in a manner similar to the known binding of FxFG nucleoporin repeats. The results in this paper provide evidence for a different binding mode. The FGDF peptide binds and changes conformation of the protruding N-terminal residues by providing hydrophobic interactions to a symmetry related molecule that facilitated crystallization of the G3BP2 isoform.


    Organizational Affiliation

    Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark. Electronic address: ok@sund.ku.dk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras GTPase-activating protein-binding protein 2
A
142Homo sapiensMutation(s): 0 
Gene Names: G3BP2 (KIAA0660)
Find proteins for Q9UN86 (Homo sapiens)
Go to Gene View: G3BP2
Go to UniProtKB:  Q9UN86
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein 3
B
8Semliki forest virusMutation(s): 0 
Find proteins for P08411 (Semliki forest virus)
Go to UniProtKB:  P08411
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.245 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 94.850α = 90.00
b = 94.850β = 90.00
c = 114.030γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-09-16 
  • Released Date: 2015-10-14 
  • Deposition Author(s): Kristensen, O.

Funding OrganizationLocationGrant Number
Alfred Benzon FoundationDenmark--
Brdr. Hartmann FoundationDenmark--
the Danish Natural Science Council (DANSCATT)Denmark--

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references