3WMU

The structure of an anti-cancer lectin mytilec apo-form from the mussel Mytilus galloprovincialis

• PDB DOI:  https://doi.org/10.2210/pdb3WMU/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mytilus galloprovincialis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-27 Released: 2014-12-03 
• Deposition Author(s): Terada, D., Kawai, F., Noguchi, H., Unzai, S., Park, S.-Y., Ozeki, Y., Tame, J.R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.163 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Literature

Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types

Terada, D., Kawai, F., Noguchi, H., Unzai, S., Hasan, I., Fujii, Y., Park, S.-Y., Ozeki, Y., Tame, J.R.H.

(2016) Sci Rep 6: 28344-28344

• PubMed: 27321048 
• DOI: https://doi.org/10.1038/srep28344
• Primary Citation of Related Structures:  
  3WMU, 3WMV


• PubMed Abstract: 
  

MytiLec is a lectin, isolated from bivalves, with cytotoxic activity against cancer cell lines that express globotriaosyl ceramide, Galα(1,4)Galβ(1,4)Glcα1-Cer, on the cell surface. Functional analysis shows that the protein binds to the disaccharide melibiose, Galα(1,6)Glc, and the trisaccharide globotriose, Galα(1,4)Galβ(1,4)Glc. Recombinant MytiLec expressed in bacteria showed the same haemagglutinating and cytotoxic activity against Burkitt's lymphoma (Raji) cells as the native form. The crystal structure has been determined to atomic resolution, in the presence and absence of ligands, showing the protein to be a member of the β-trefoil family, but with a mode of ligand binding unique to a small group of related trefoil lectins. Each of the three pseudo-equivalent binding sites within the monomer shows ligand binding, and the protein forms a tight dimer in solution. An engineered monomer mutant lost all cytotoxic activity against Raji cells, but retained some haemagglutination activity, showing that the quaternary structure of the protein is important for its cellular effects.

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Organizational Affiliation: 

Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.94 kDa 
• Atom Count: 2,817 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	153	Mytilus galloprovincialis	Mutation(s): 1
UniProt
Find proteins for B3EWR1 (Mytilus galloprovincialis) Explore B3EWR1  Go to UniProtKB:  B3EWR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.163 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.725	α = 90
b = 41.507	β = 108.45
c = 68.831	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Terada, D., Kawai, F., Noguchi, H., Unzai, S., Park, S.-Y., Ozeki, Y., Tame, J.R.H.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references