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 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1016/j.cell.2015.09.056
  • Primary Citation of Related Structures:  
    4PIF, 4PIK, 4PIT, 4PIU

  • 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, significantly reduces its mitogenicity, while preserving its broad-spectrum antiviral potency ...

    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: 

    Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: dmarkov@umich.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ripening-associated protein
A, B, C, D
149Musa acuminataMutation(s): 1 
UniProt
Find proteins for O22321 (Musa acuminata)
Explore O22321 
Go to UniProtKB:  O22321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO22321
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
E, F, G, H, I
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900111
Query on PRD_900111
E, F, G, H, I
2alpha-alpha-mannobioseOligosaccharide / Metabolism 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 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.613α = 90
b = 94.963β = 97.6
c = 63.054γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary