6GKT | pdb_00006gkt

X-ray structure of a non-autocrystallizing galectin-10 variant, Gal10-Tyr69Glu

PDB DOI: https://doi.org/10.2210/pdb6GKT/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-05-21 Released: 2019-06-05
Deposition Author(s): Verstraete, K., Verschueren, K., Savvides, S.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.172 (Depositor), 0.178 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Protein crystallization promotes type 2 immunity and is reversible by antibody treatment.

Persson, E.K., Verstraete, K., Heyndrickx, I., Gevaert, E., Aegerter, H., Percier, J.M., Deswarte, K., Verschueren, K.H.G., Dansercoer, A., Gras, D., Chanez, P., Bachert, C., Goncalves, A., Van Gorp, H., De Haard, H., Blanchetot, C., Saunders, M., Hammad, H., Savvides, S.N., Lambrecht, B.N.

(2019) Science 364

PubMed: 31123109 Search on PubMed
DOI: https://doi.org/10.1126/science.aaw4295
Primary Citation Related Structures:
6GKQ, 6GKS, 6GKT, 6GKU, 6GLW, 6GLX, 6QRN

PubMed Abstract:
Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such as asthma. We found that CLCs derived from patients showed crystal packing and Gal10 structure identical to those of Gal10 crystals grown in vitro. When administered to the airways, crystalline Gal10 stimulated innate and adaptive immunity and acted as a type 2 adjuvant. By contrast, a soluble Gal10 mutein was inert. Antibodies directed against key epitopes of the CLC crystallization interface dissolved preexisting CLCs in patient-derived mucus within hours and reversed crystal-driven inflammation, goblet-cell metaplasia, immunoglobulin E (IgE) synthesis, and bronchial hyperreactivity (BHR) in a humanized mouse model of asthma. Thus, protein crystals may promote hallmark features of asthma and are targetable by crystal-dissolving antibodies.

Organizational Affiliation

Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.

Macromolecule Content

Total Structure Weight: 101.48 kDa
Atom Count: 7,523
Modeled Residue Count: 836
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-10	A, B, C, D, E A, B, C, D, E, F	144	Homo sapiens	Mutation(s): 0 Gene Names: CLC, LGALS10, LGALS10A
UniProt & NIH Common Fund Data Resources
Find proteins for Q05315 (Homo sapiens) Explore Q05315 Go to UniProtKB: Q05315
PHAROS: Q05315 GTEx: ENSG00000105205
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05315
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain M [auth E] MOL2 format, chain M [auth E] mmCIF format, chain M [auth E]	M [auth E]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Interactions & Density Focus chain M [auth E]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth F] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth F] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A]	G [auth A] H [auth A] J [auth B] K [auth C] L [auth C] G [auth A], H [auth A], J [auth B], K [auth C], L [auth C], N [auth E], O [auth F], P [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]