9ENA | pdb_00009ena

Lysosomal glucocerebrosidase in complex with a stabilizing nanobody

• PDB DOI: https://doi.org/10.2210/pdb9ENA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Lama glama
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-12 Released: 2025-06-04 
• Deposition Author(s): Dal Maso, T., Versees, W.
• Funding Organization(s): Michael J. Fox Foundation, Research Foundation - Flanders (FWO), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Models: experimental

Literature

Developing nanobodies as allosteric molecular chaperones of glucocerebrosidase function.

Dal Maso, T., Sinisgalli, C., Zilio, G., Franzin, E., Tessari, I., Pardon, E., Steyaert, J., Ballet, S., Greggio, E., Versees, W., Plotegher, N.

(2025) Nat Commun 16: 4890-4890

• PubMed: 40425544 
• DOI: https://doi.org/10.1038/s41467-025-60134-4
• Primary Citation Related Structures: 
  9ENA


• PubMed Abstract: 
  

  The enzyme glucocerebrosidase (GCase) catalyses the hydrolysis of glucosylceramide to glucose and ceramide within lysosomes. Homozygous or compound heterozygous mutations in the GCase-encoding GBA1 gene cause the lysosomal storage disorder Gaucher disease, while heterozygous and homozygous mutations are the most frequent genetic risk factor for Parkinson's disease. These mutations commonly affect GCase stability, trafficking or activity. Here, we report the development and characterization of nanobodies (Nbs) targeting and acting as molecular chaperones for GCase. We identify several Nb families that bind with nanomolar affinity to GCase. Based on biochemical characterization, we group the Nbs in two classes: Nbs that improve the activity of the enzyme and Nbs that increase GCase stability in vitro. A selection of the most promising Nbs is shown to improve GCase function in cell models and positively impact the activity of the N370S mutant GCase. These results lay the foundation for the development of new therapeutic routes.

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Organizational Affiliation: 
• VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.
Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
Department of Biology, University of Padova, Padova, Italy.
Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium.
Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy.
VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium. [e-mail].
Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium. [e-mail].
Department of Biology, University of Padova, Padova, Italy. [e-mail].
Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.95 kDa 
• Atom Count: 5,853 
• Modeled Residue Count: 627 
• Deposited Residue Count: 639 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A	497	Homo sapiens	Mutation(s): 1  Gene Names: GBA, GC, GLUC EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (PDB Primary Data), 3.2.1.104 (PDB Primary Data), 3.2.1.46 (UniProt), 3.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens) Explore P04062  Go to UniProtKB:  P04062
PHAROS:  P04062 GTEx:  ENSG00000177628
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P04062-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: B	B	142	Lama glama	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.209	α = 90
b = 113.209	β = 90
c = 257.373	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Dal Maso, T., Versees, W.

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Funding Organization	Location	Grant Number
Michael J. Fox Foundation	United States	MJFF-17240
Michael J. Fox Foundation	United States	MJFF-020706
Research Foundation - Flanders (FWO)	Belgium	G031324N
Other private	Belgium	SRP50
Other private	Belgium	SRP95

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release