6VTP

Crystal structure of G16C human Galectin-7 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7.

Pham, N.T.H.Letourneau, M.Fortier, M.Begin, G.Al-Abdul-Wahid, M.S.Pucci, F.Folch, B.Rooman, M.Chatenet, D.St-Pierre, Y.Lague, P.Calmettes, C.Doucet, N.

(2021) J Biol Chem 297: 101308-101308

  • DOI: 10.1016/j.jbc.2021.101308
  • Primary Citation of Related Structures:  
    6VTO, 6VTP, 6VTQ, 6VTR, 6VTS

  • PubMed Abstract: 
  • The design of allosteric modulators to control protein function is a key objective in drug discovery programs. Altering functionally essential allosteric residue networks provides unique protein family subtype specificity, minimizes unwanted off-target effects, and helps avert resistance acquisition typically plaguing drugs that target orthosteric sites ...

    The design of allosteric modulators to control protein function is a key objective in drug discovery programs. Altering functionally essential allosteric residue networks provides unique protein family subtype specificity, minimizes unwanted off-target effects, and helps avert resistance acquisition typically plaguing drugs that target orthosteric sites. In this work, we used protein engineering and dimer interface mutations to positively and negatively modulate the immunosuppressive activity of the pro-apoptotic human galectin-7 (GAL-7). Using the PoPMuSiC and BeAtMuSiC algorithms, mutational sites and residue identity were computationally probed and predicted to either alter or stabilize the GAL-7 dimer interface. By designing a covalent disulfide bridge between protomers to control homodimer strength and stability, we demonstrate the importance of dimer interface perturbations on the allosteric network bridging the two opposite glycan binding sites on GAL-7, resulting in control of induced apoptosis in Jurkat T cells. Molecular investigation of G16X GAL-7 variants using X-ray crystallography, biophysical, and computational characterization illuminates residues involved in dimer stability and allosteric communication, along with discrete long-range dynamic behaviors involving loops 1, 3 and 5. We show that perturbing the protein-protein interface between GAL-7 protomers can modulate its biological function, even when the overall structure and ligand binding affinity remains unaltered. This study highlights new avenues for the design of galectin-specific modulators influencing both glycan-dependent and glycan-independent interactions.


    Organizational Affiliation

    Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, QC, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC, Canada. Electronic address: nicolas.doucet@inrs.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-7A, B135Homo sapiensMutation(s): 1 
Gene Names: LGALS7PIG1LGALS7B
UniProt & NIH Common Fund Data Resources
Find proteins for P47929 (Homo sapiens)
Explore P47929 
Go to UniProtKB:  P47929
PHAROS:  P47929
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.6α = 90
b = 67.15β = 90
c = 71.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN 2016-05557
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM105978
Fonds de Recherche du Quebec - Sante (FRQS)CanadaResearch Scholar Senior Career Award (281993)
Fonds de Recherche du Quebec - Sante (FRQS)CanadaJunior 1 (251848)
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2017-06091
Fonds de Recherche du Quebec - Sante (FRQS)CanadaDoctoral Training scholarship (287239)

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2021-11-24
    Changes: Database references