9SRK | pdb_00009srk

Structure of collectin-11 (CL-11) carbohydrate-recognition domain in complex with L-fucose

PDB DOI: https://doi.org/10.2210/pdb9SRK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-24 Released: 2025-11-05
Deposition Author(s): Wallis, R., Alrehaili, A.F.M., Sacks, S.H., klavinskis, L.S.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.198 (Depositor), 0.202 (DCC)
R-Value Work:
0.158 (Depositor), 0.163 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Glycan recognition by collectin-11 drives SARS-CoV-2 infectivity and membrane injury of respiratory epithelial cells.

Polycarpou, A., Wagner-Gamble, T., Greenlaw, R., O'Neill, L., Kanabar, V., Alrehaili, A., Jeon, Y., Baker, J., Bafadhel, M., Khan, H., Malim, M.H., Romano, M., Farrar, C.A., Smolarek, D., Martinez-Nunez, R., Doores, K.J., Wallis, R., Klavinskis, L.S., Sacks, S.H.

(2025) Proc Natl Acad Sci U S A 122: e2521209122-e2521209122

PubMed: 41134631 Search on PubMed
DOI: https://doi.org/10.1073/pnas.2521209122
Primary Citation Related Structures:
9SRK

PubMed Abstract:
SARS-CoV-2 respiratory-tract infection affects both vaccinated and unvaccinated persons suggesting factors besides adaptive immunity are operative. We investigated the role of collectin-11 (CL-11), an epithelial-secreted carbohydrate-binding lectin that drives innate immunity and eliminates pathogens by complement activation. SARS-CoV-2, despite binding CL-11 to activate complement, was resistant to lysis. Remarkably, opsonization by CL-11 enhanced virus production by infected respiratory epithelial cells independently of complement. Furthermore, infected cells expressing SARS-CoV-2 spike protein displayed enhanced vulnerability to CL-11 binding and membrane attack by complement. The mechanism of enhanced infectivity was ablated in the presence of L-fucose, which occupied the extended carbohydrate-binding cleft of CL-11 in a crystallographic analysis of complexes between L-fucose and CL-11. Our study suggests pathogenicity of SARS-CoV-2 is related to complement-resistance together with enhanced infectivity and injury of respiratory epithelial cells mediated by locally released CL-11.

Organizational Affiliation

Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College, London SE1 9RT, United Kingdom.

Macromolecule Content

Total Structure Weight: 30.25 kDa
Atom Count: 2,287
Modeled Residue Count: 252
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collectin-11	A, B	127	Homo sapiens	Mutation(s): 0 Gene Names: COLEC11, UNQ596/PRO1182
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWP8 (Homo sapiens) Explore Q9BWP8 Go to UniProtKB: Q9BWP8
PHAROS: Q9BWP8 GTEx: ENSG00000118004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BWP8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUL (Subject of Investigation/LOI) Query on FUL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], O [auth B], Q [auth B]	beta-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-KGJVWPDLSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain Q [auth B]
FUC (Subject of Investigation/LOI) Query on FUC Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	F [auth A], J [auth A], N [auth B], P [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth B]
TRS (Subject of Investigation/LOI) Query on TRS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] K [auth B] L [auth B] C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]