8B8F

Atomic structure of the beta-trefoil domain of the Laccaria bicolor lectin LBL in complex with lactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Atomic crystal structure and sugar specificity of a beta-trefoil lectin domain from the ectomycorrhizal basidiomycete Laccaria bicolor.

Acebron, I.Campanero-Rhodes, M.A.Solis, D.Menendez, M.Garcia, C.Lillo, M.P.Mancheno, J.M.

(2023) Int J Biol Macromol 233: 123507-123507

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.123507
  • Primary Citation of Related Structures:  
    8B8F, 8B97

  • PubMed Abstract: 

    Lectins from fruiting bodies are a diverse group of sugar-binding proteins from mushrooms that face the biologically relevant challenge of discriminating self- from non-self carbohydrate structures, therefore providing a basis for an innate defence system. Such a system entails both detection and destruction of invaders and/or feeders, and in contrast to more complex organisms with immense immune systems, these two functions normally rely on multitasking lectins, namely, lectins with different functional modules. Here, we present a novel fungal lectin, LBL, from the basidiomycete Laccaria bicolor. Using a diverse set of biophysical techniques, we unveil the fine details of the sugar-binding specificity of the N-terminal β-trefoil of LBL (LBL 152 ), whose structure has been determined at the highest resolution so far reported for such a fold. LBL 152 binds complex poly-N-Acetyllactosamine polysaccharides and also robust LBL 152 binding to Caenorhabditis elegans and Drosophila melanogaster cellular extracts was detected in microarray assays, with a seeming preference for the fruit fly adult and pupa stages over the larva stage. Prediction of the structure of the C-terminal part of LBL with AlphaFold reveals a tandem repeat of two structurally almost identical domains of around 110 amino acids each, despite sharing low sequence conservation.


  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal beta-trefoil domain of the lectin LBL from Laccaria bicolor152Laccaria bicolor S238N-H53Mutation(s): 0 
Gene Names: LACBIDRAFT_318163
UniProt
Find proteins for B0D650 (Laccaria bicolor (strain S238N-H82 / ATCC MYA-4686))
Explore B0D650 
Go to UniProtKB:  B0D650
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0D650
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranoseB [auth C],
C [auth B],
D
2N/A
Glycosylation Resources
GlyTouCan:  G88362QR
GlyCosmos:  G88362QR
GlyGen:  G88362QR
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
E, F, G
2N/A
Glycosylation Resources
GlyTouCan:  G84224TW
GlyCosmos:  G84224TW
GlyGen:  G84224TW
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.53α = 90
b = 61.27β = 90
c = 44.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2010-17929/BMC
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-099985-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description