9QVU

Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepI-(1,5)-KdoI ligand

Summary for 9QVU

• Entry DOI: 10.2210/pdb9qvu/pdb
• Descriptor: Pulmonary surfactant-associated protein D, CALCIUM ION, L-glycero-alpha-D-manno-heptopyranose, ... (4 entities in total)
• Functional Keywords: trimeric recombinant collectin fragment, neck+crd, alpha-helical coiled coil, carbohydrate recognition domain, lectin, sugar binding protein, surfactant protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 57285.94

Authors

Shrive, A.K.,Greenhough, T.J.,Williams, H.M. (deposition date: 2025-04-12, release date: 2026-03-04)

Primary citation

Williams, H.M.,Watson, A.,Madsen, J.,Clark, H.W.,Hood, D.W.,Oscarson, S.,Greenhough, T.J.,Shrive, A.K.
Phosphorylation of inner core heptose is a major determinant of bacterial surface lipopolysaccharide recognition by the innate immune protein hSP-D.
J.Biol.Chem., :111307-111307, 2026

PubMed Abstract: The innate immune protein human surfactant protein D (SP-D) recognises pathogens in the lungs via binding to carbohydrate surface structures. SP-D targets gram-negative bacterial lipopolysaccharide via calcium-dependent binding, preferentially to the inner core heptose (HepI). To further investigate this recognition, we have determined the high-resolution crystal structures of a trimeric recombinant fragment of human SP-D complexed with synthetic di- and trisaccharides, HepI-Kdo, HepIII-HepII-HepI, and HepII-HepI phosphorylated at either HepI or HepII, inner core lipopolysaccharide motifs common to many gram-negative bacteria. In contrast to acid-hydrolysed lipopolysaccharide used in several previous studies, these synthetic saccharides allow presentation of both the innermost Kdo in its natural pyranose form and heptose phosphorylation. The structures confirm the flexibility of SP-D to adopt alternative binding modes when the preferred epitope is not available, reveal a preference for recognition of the reducing terminal heptose (HepI) via the glyceryl group, indicate that a single Kdo attached to HepI does not have a significant role in ligand recognition, and provide evidence that heptose phosphorylation is a major determinant of recognition. The disaccharide with HepII O4' phosphorylation binds via the preferred HepI glyceryl-hydroxyls, while HepI O4' phosphorylation reveals HepII binding via the pyranose ring O3' and O4' hydroxyls, which would not be possible with the usual HepII O3' link to the outer core. The ability of HepI O4' phosphorylation to prevent preferred HepI recognition suggests a role for heptose phosphorylation in shielding the bacterial LPS inner core from immune recognition.

PubMed: 41724382
DOI: 10.1016/j.jbc.2026.111307

Experimental method

X-RAY DIFFRACTION (1.75 Å)