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 
  • R-Value Observed: 0.250 

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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
  • Primary Citation of Related Structures:  
    5DRV

  • 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 highly similar to the homodimeric N-terminal domains of the G3BP1 and Rasputin proteins ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras GTPase-activating protein-binding protein 2A142Homo sapiensMutation(s): 0 
Gene Names: G3BP2KIAA0660
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UN86 (Homo sapiens)
Explore Q9UN86 
Go to UniProtKB:  Q9UN86
PHAROS:  Q9UN86
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3B8Semliki Forest virusMutation(s): 0 
EC: 2.1.1 (UniProt), 2.7.7 (UniProt), 3.1.3.33 (UniProt), 3.4.22 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 3.1.3.84 (UniProt), 2.7.7.19 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P08411 (Semliki forest virus)
Explore P08411 
Go to UniProtKB:  P08411
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.250 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.85α = 90
b = 94.85β = 90
c = 114.03γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

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