8VCS | pdb_00008vcs

Crystal structure of the oligomeric rMcL-1 in complex with lactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.188 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8VCS

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A mytilectin from Mytilus californianus: Study of its unique galactoside interactions, oligomerization patterns, and antifungal activity.

Loera-Rubalcava, J.Garcia-Maldonado, E.Rodriguez-Romero, A.Quintero-Martinez, A.Macias-Rubalcava, M.L.Cano-Sanchez, P.Ramirez-Rodriguez, M.A.Espinosa-Perez, G.Hernandez-Santoyo, A.

(2025) Int J Biol Macromol 308: 142338-142338

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.142338
  • Primary Citation Related Structures: 
    8VCK, 8VCM, 8VCO, 8VCP, 8VCQ, 8VCS, 8VCU

  • PubMed Abstract: 

    In marine invertebrate such as bivalve mollusks, lectins play a critical rol in the immune system, defending against pathogens. A novel family of lectins, named mytilectins, has been discovered in these organisms. They are noted for their antifungal, antibacterial, and anticancer properties, suggesting substantial potential for biomedical and biotechnological applications. In this study, we describe rMcL-1, a mytilectin from the mussel Mytilus californianus. We explored the binding mechanisms using crystallographic data with five different galactosides, highlighting rMcL-1's preference for α-galactosides. By analyzing amino acid variations in its three carbohydrate-binding sites, we assessed their impact on binding affinity and specificity. Interestingly, rMcL-1 is capable of binding non-galactosides, and ligands with lower affinity, such as lactose, induce significant conformational changes in specific binding sites. A novel binding site at the dimer interface was identified in the presence of lactulose. Co-crystallization experiments demonstrated that ligand binding promotes oligomerization, with the resulting quaternary structure varying depending on the sugar involved. An analysis of the puckering parameters and transglycosidic dihedral angles of the glycan moieties associated with oligomeric rMcL-1 revealed consistent conformational preferences in lactulose moieties, while raffinose and lactose exhibited greater variability. Additionally, rMcL-1 exhibited antifungal activity against several phytopathogenic fungi, including Alternaria alternata, Fusarium oxysporum, Phytophthora capsici, and Pythium aphanidermatum. Overall, this study enhances our understanding of the molecular mechanisms underlying the diverse activities of mytilectins and may aid in the design of artificial lectins with specific and improved binding properties.


  • Organizational Affiliation
    • Instituto de Química, Departamento de Química de Biomacromoléculas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.

Macromolecule Content 

  • Total Structure Weight: 143.77 kDa 
  • Atom Count: 10,807 
  • Modeled Residue Count: 1,203 
  • Deposited Residue Count: 1,216 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactose-binding lectin
A, B, C, D, E
A, B, C, D, E, F, G, H
152Mytilus californianusMutation(s): 3 
UniProt
Find proteins for A0A0P0E482 (Mytilus californianus)
Explore A0A0P0E482 
Go to UniProtKB:  A0A0P0E482
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P0E482
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAL
(Subject of Investigation/LOI)

Query on GAL



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
CA [auth F]
DA [auth G]
FA [auth H]
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth G],
FA [auth H],
T [auth A],
U [auth A],
V [auth B],
W [auth C],
X [auth C],
Y [auth D],
Z [auth D]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
EA [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.188 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.908α = 90
b = 77.871β = 90.05
c = 155.796γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedMexico--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references
  • Version 1.2: 2025-05-21
    Changes: Database references