4PIT

Crystal Structure of Banana Lectin H84T bound to dimannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineering a Therapeutic Lectin by Uncoupling Mitogenicity from Antiviral Activity.

Swanson, M.D.Boudreaux, D.M.Salmon, L.Chugh, J.Winter, H.C.Meagher, J.L.Andre, S.Murphy, P.V.Oscarson, S.Roy, R.King, S.Kaplan, M.H.Goldstein, I.J.Tarbet, E.B.Hurst, B.L.Smee, D.F.de la Fuente, C.Hoffmann, H.H.Xue, Y.Rice, C.M.Schols, D.Garcia, J.V.Stuckey, J.A.Gabius, H.J.Al-Hashimi, H.M.Markovitz, D.M.

(2015) Cell 163: 746-758

  • DOI: 10.1016/j.cell.2015.09.056
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A key effector route of the Sugar Code involves lectins that exert crucial regulatory controls by targeting distinct cellular glycans. We demonstrate that a single amino-acid substitution in a banana lectin, replacing histidine 84 with a threonine, s ...

    A key effector route of the Sugar Code involves lectins that exert crucial regulatory controls by targeting distinct cellular glycans. We demonstrate that a single amino-acid substitution in a banana lectin, replacing histidine 84 with a threonine, significantly reduces its mitogenicity, while preserving its broad-spectrum antiviral potency. X-ray crystallography, NMR spectroscopy, and glycocluster assays reveal that loss of mitogenicity is strongly correlated with loss of pi-pi stacking between aromatic amino acids H84 and Y83, which removes a wall separating two carbohydrate binding sites, thus diminishing multivalent interactions. On the other hand, monovalent interactions and antiviral activity are preserved by retaining other wild-type conformational features and possibly through unique contacts involving the T84 side chain. Through such fine-tuning, target selection and downstream effects of a lectin can be modulated so as to knock down one activity, while preserving another, thus providing tools for therapeutics and for understanding the Sugar Code.


    Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA. Electronic address: ha57@duke.edu.,Department of Chemistry, Université du Québec à Montréal, Montréal, Québec H3C 3P8, Canada.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, 3000 Leuven, Belgium.,Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.,Rockefeller University, New York, NY 10065, USA.,Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA.,Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 Munich, Germany.,Department of Biochemistry, Duke University, Durham, NC 27710, USA.,Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Division of Infectious Diseases, Department of Medicine and UNC AIDS Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.,School of Chemistry, National University of Ireland, Galway, Ireland.,Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: dmarkov@umich.edu.,Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.,Division of Infectious Diseases, Department of Medicine and UNC AIDS Center, University of North Carolina, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ripening-associated protein
A, B, C, D
149Musa acuminataMutation(s): 1 
Find proteins for O22321 (Musa acuminata)
Go to UniProtKB:  O22321
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.613α = 90.00
b = 94.963β = 97.60
c = 63.054γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTERrefinement
BUSTER-TNTrefinement
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description