8UX7 | pdb_00008ux7

Dioclea megacarpa lectin (DmegA) complexed with X-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.248 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.208 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Crystal structure, glycan specificity, and induction of cellular stress by the legume lectin DmegA.

Osterne, V.J.S.Ervijn, L.Oliveira, M.V.Pinto-Junior, V.R.Serna, S.Reichardt, N.C.Nascimento, K.S.Van Damme, E.J.M.Cavada, B.S.

(2026) Int J Biol Macromol 358: 151795-151795

  • DOI: https://doi.org/10.1016/j.ijbiomac.2026.151795
  • Primary Citation Related Structures: 
    8UX7

  • PubMed Abstract: 

    The precise molecular mechanisms translating glycan recognition by plant lectins into cancer cell death remain incompletely understood. To address this gap, this study examines the cytotoxic response elicited by the mannose-specific legume lectin DmegA by integrating structural biology, glycan profiling, and cellular assays to map events from cell surface binding to apoptosis. The 2.4 Å crystal structure reveals a canonical ConA-like fold with conserved carbohydrate-recognition and Ca 2+ /Mn 2+ coordination sites. Glycan microarray and molecular docking analyses indicate preferential recognition of mannose-rich N-glycan motifs, including the core trimannoside of N-glycans, consistent with the interaction of the lectin with a broad range of glycoproteins. Glycan-dependent internalization of DmegA in PANC-1 cells was associated with increased EDEM transcript levels, whereas no statistically significant change in CHOP transcript levels was detected, alongside elevated ROS levels and caspase activation. The pro-apoptotic gene PUMA was upregulated, suggesting a potential connection between cellular stress responses and mitochondrial apoptosis. While the observation of EDEM induction in the absence of statistically significant CHOP upregulation represents a low-power preliminary finding, the combined data support a cellular phenotype characterized by oxidative stress, caspase activation, and ER-associated transcriptional changes. Given its broad glycan recognition and lack of tumor selectivity, DmegA is not directly suitable for therapeutic applications, but the structural and mechanistic insights provided here inform future engineering or targeting strategies aimed at improving lectin selectivity.


  • Organizational Affiliation
    • BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, 60020-181, CE, Brazil.

Macromolecule Content 

  • Total Structure Weight: 52.26 kDa 
  • Atom Count: 3,690 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 474 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dioclea megacarpa lectin
A, B
237Macropsychanthus megacarpusMutation(s): 0 
UniProt
Find proteins for B3EWJ2 (Macropsychanthus sclerocarpus)
Explore B3EWJ2 
Go to UniProtKB:  B3EWJ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3EWJ2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XMM
(Subject of Investigation/LOI)

Query on XMM



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.248 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.35α = 90
b = 109.414β = 90
c = 126.364γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Coordination for the Improvement of Higher Education PersonnelBrazil--
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--
Research Foundation - Flanders (FWO)Belgium12T4622N

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Database references, Structure summary