6TRV

Structure of SapL1 lectin in complex with alpha methyl fucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 

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Literature

Biochemical and structural studies of target lectin SapL1 from the emerging opportunistic microfungus Scedosporium apiospermum.

Martinez-Alarcon, D.Balloy, V.Bouchara, J.P.Pieters, R.J.Varrot, A.

(2021) Sci Rep 11: 16109-16109

  • DOI: https://doi.org/10.1038/s41598-021-95008-4
  • Primary Citation of Related Structures:  
    6TRV

  • PubMed Abstract: 

    Scedosporium apiospermum is an emerging opportunistic fungal pathogen responsible for life-threatening infections in humans. Host-pathogen interactions often implicate lectins that have become therapeutic targets for the development of carbohydrate mimics for antiadhesive therapy. Here, we present the first report on the identification and characterization of a lectin from S. apiospermum named SapL1. SapL1 was found using bioinformatics as a homolog to the conidial surface lectin FleA from Aspergillus fumigatus known to play a role in the adhesion to host glycoconjugates present in human lung epithelium. In our strategy to obtain recombinant SapL1, we discovered the importance of osmolytes to achieve its expression in soluble form in bacteria. Analysis of glycan arrays indicates specificity for fucosylated oligosaccharides as expected. Submicromolar affinity was measured for fucose using isothermal titration calorimetry. We solved SapL1 crystal structure in complex with α-methyl-L-fucoside and analyzed its structural basis for fucose binding. We finally demonstrated that SapL1 binds to bronchial epithelial cells in a fucose-dependent manner. The information gathered here will contribute to the design and development of glycodrugs targeting SapL1.


  • Organizational Affiliation

    Univ. Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinA [auth AAA],
B [auth BBB]
297Scedosporium apiospermumMutation(s): 0 
Gene Names: SAPIO_CDS9261
UniProt
Find proteins for A0A084FYP2 (Pseudallescheria apiosperma)
Explore A0A084FYP2 
Go to UniProtKB:  A0A084FYP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A084FYP2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MFU (Subject of Investigation/LOI)
Query on MFU

Download Ideal Coordinates CCD File 
C [auth AAA]
D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
M [auth BBB],
N [auth BBB],
O [auth BBB],
P [auth BBB]
methyl alpha-L-fucopyranoside
C7 H14 O5
OHWCAVRRXKJCRB-CXNFULCWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth AAA]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
Q [auth BBB]
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
Q [auth BBB],
R [auth BBB],
S [auth BBB]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.064α = 90
b = 45.664β = 105.054
c = 83.485γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFrance765581

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Derived calculations, Refinement description