8P8T | pdb_00008p8t

Ex vivo Ym2 crystal structure

• PDB DOI: https://doi.org/10.2210/pdb8P8T/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2023-06-02 Released: 2024-01-17 
• Deposition Author(s): Verschueren, K.H.G., Verstraete, K., Heyndrickx, I., Smole, U., Aegerter, H., Savvides, S.N., Lambrecht, B.N.
• Funding Organization(s): European Research Council (ERC), Research Foundation - Flanders (FWO)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Ym1 protein crystals promote type 2 immunity.

Heyndrickx, I., Deswarte, K., Verstraete, K., Verschueren, K.H.G., Smole, U., Aegerter, H., Dansercoer, A., Hammad, H., Savvides, S.N., Lambrecht, B.N.

(2024) Elife 12

• PubMed: 38194250 
• DOI: https://doi.org/10.7554/eLife.90676
• Primary Citation Related Structures: 
  8P8Q, 8P8R, 8P8S, 8P8T


• PubMed Abstract: 
  

  Spontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Although mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded by Chil3 and Chil4 and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography as in vivo native crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs.

---

Organizational Affiliation: 
• Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.
Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
Department of Pulmonary Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 45.11 kDa 
• Atom Count: 3,251 
• Modeled Residue Count: 374 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-like protein 4	A	402	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q91Z98 (Mus musculus) Explore Q91Z98  Go to UniProtKB:  Q91Z98

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.261	α = 90
b = 60.205	β = 94.24
c = 60.173	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Verschueren, K.H.G., Verstraete, K., Heyndrickx, I., Smole, U., Aegerter, H., Savvides, S.N., Lambrecht, B.N.

---

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	789384
Research Foundation - Flanders (FWO)	Belgium	G0H1222N

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Structure summary