8PE2

Crystal structure of Gel4 in complex with Nanobody 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


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Literature

Broad protection against invasive fungal disease from a nanobody targeting the active site of fungal b-1,3-glucanosyltransferases.

Redrado-Hernandez, S.Macias-Leon, J.Castro-Lopez, J.Sanz, A.B.Dolader, E.Arias, M.Gonzalez-Ramirez, A.M.Sanchez-Navarro, D.Petryk, Y.Farkas, V.Vincke, C.Muyldermans, S.Garcia-Barbazan, I.Del Agua, C.Zaragoza, O.Arroyo, J.Pardo, J.Galvez, E.Hurtado-Guerrero, R.

(2024) Angew Chem Int Ed Engl : e202405823-e202405823

  • DOI: https://doi.org/10.1002/anie.202405823
  • Primary Citation of Related Structures:  
    8PE1, 8PE2

  • PubMed Abstract: 

    Invasive fungal disease accounts for ~3.8 million deaths annually, an unacceptable rate that urgently prompts the discovery of new knowledge-driven treatments. We report the use of camelid single-domain nanobodies (Nbs) against fungal β-1,3-glucanosyltransferases (Gel) involved in β-1,3-glucan transglycosylation. Crystal structures of two Nbs with Gel4 from Aspergillus fumigatus revealed binding to a dissimilar CBM43 domain and a highly conserved catalytic domain across fungal species, respectively. Anti-Gel4 active site Nb3 showed significant antifungal efficacy in vitro and in vivo prophylactically and therapeutically against different A. fumigatus and Cryptococcus neoformans isolates, reducing the fungal burden and disease severity, thus significantly improving immunocompromised animal survival. Notably, C. deneoformans (serotype D) strains were more susceptible to Nb3 and genetic Gel deletion than C. neoformans (serotype A) strains, indicating a key role for β-1,3-glucan remodelling in C. deneoformans survival. These findings add new insights about the role of b-1,3-glucan in fungal biology and demonstrate the potential of nanobodies in targeting fungal enzymes to combat invasive fungal diseases.


  • Organizational Affiliation

    Instituto de Carboquimica, Instituto de Carboquimica, SPAIN.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1,3-beta-glucanosyltransferase451Aspergillus fumigatusMutation(s): 0 
Gene Names: CDV57_08969
UniProt
Find proteins for A0A229W401 (Aspergillus fumigatus)
Explore A0A229W401 
Go to UniProtKB:  A0A229W401
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A229W401
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 3120Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A],
I [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A],
H [auth A]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.992α = 90
b = 96.992β = 90
c = 106.625γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)Spain--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release