6LF2 | pdb_00006lf2

SeviL bound to asialo-GM1 saccharide

• PDB DOI: https://doi.org/10.2210/pdb6LF2/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mytilisepta virgata
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-28 Released: 2020-12-02 
• Deposition Author(s): Kamata, K., Ozeki, Y., Park, S.-Y., Tame, J.R.H.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata.

Kamata, K., Mizutani, K., Takahashi, K., Marchetti, R., Silipo, A., Addy, C., Park, S.Y., Fujii, Y., Fujita, H., Konuma, T., Ikegami, T., Ozeki, Y., Tame, J.R.H.

(2020) Sci Rep 10: 22102-22102

• PubMed: 33328520 
• DOI: https://doi.org/10.1038/s41598-020-78926-7
• Primary Citation Related Structures: 
  6LF1, 6LF2


• PubMed Abstract: 
  

  SeviL is a recently isolated lectin found to bind to the linear saccharides of the ganglioside GM1b (Neu5Ac[Formula: see text](2-3)Gal[Formula: see text](1-3)GalNAc[Formula: see text](1-4)Gal[Formula: see text](1-4)Glc) and its precursor, asialo-GM1 (Gal[Formula: see text](1-3)GalNAc[Formula: see text](1-4)Gal[Formula: see text](1-4)Glc). The crystal structures of recombinant SeviL have been determined in the presence and absence of ligand. The protein belongs to the [Formula: see text]-trefoil family, but shows only weak sequence similarity to known structures. SeviL forms a dimer in solution, with one binding site per subunit, close to the subunit interface. Molecular details of glycan recognition by SeviL in solution were analysed by ligand- and protein-based NMR techniques as well as ligand binding assays. SeviL shows no interaction with GM1 due to steric hindrance with the sialic acid branch that is absent from GM1b. This unusual specificity makes SeviL of great interest for the detection and control of certain cancer cells, and cells of the immune system, that display asialo-GM1.

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Organizational Affiliation: 
• Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan.
Department of Chemical Sciences, Università di Napoli Federico II, Via Cintia 4, 80126, Naples, Italy.
Department of Pharmacy, Graduate School of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298, Japan.
Laboratory of Glycobiology and Marine Biochemistry, Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa, 236-0027, Japan.
Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.11 kDa 
• Atom Count: 2,357 
• Modeled Residue Count: 256 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SeviL	A, B	132	Mytilisepta virgata	Mutation(s): 0
UniProt
Find proteins for A0A646QV53 (Mytilisepta virgata) Explore A0A646QV53  Go to UniProtKB:  A0A646QV53

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan: G21856LC GlyCosmos: G21856LC GlyGen: G21856LC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.59	α = 90
b = 61.59	β = 90
c = 136.783	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Kamata, K., Ozeki, Y., Park, S.-Y., Tame, J.R.H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JP18H02413

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description