4FCM

Crystal structure of the NTF2-like domain of human G3BP1 in complex with a peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity.

Vognsen, T.Moller, I.R.Kristensen, O.

(2013) Plos One 8: e80947-e80947

  • DOI: 10.1371/journal.pone.0080947
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both ...

    Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded form of the G3BP1 NTF2-like domain was solved in two crystal forms to resolutions of 1.6 and 3.3 Å in space groups P212121 and P6322 based on two different constructs, residues 1-139 and 11-139, respectively. Crystal packing of the N-terminal residues against a symmetry related molecule in the P212121 crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design.


    Organizational Affiliation

    Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras GTPase-activating protein-binding protein 1
A, B
142Homo sapiensMutation(s): 0 
Gene Names: G3BP1 (G3BP)
EC: 3.6.4.12, 3.6.4.13
Find proteins for Q13283 (Homo sapiens)
Go to Gene View: G3BP1
Go to UniProtKB:  Q13283
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin repeat peptide
C, D
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.780α = 90.00
b = 71.490β = 90.00
c = 89.500γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHENIXphasing
MAR345data collection
PHENIXmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Data collection, Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description