9NBG

H-1 Parvovirus VLP - Glycan [s(Lex)2]

This is a non-PDB format compatible entry.

Summary for 9NBG

• Entry DOI: 10.2210/pdb9nbg/pdb
• EMDB information: 49228
• Related PRD ID: PRD_900067
• Descriptor: Major capsid protein, N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose (2 entities in total)
• Functional Keywords: icosahedron, virus, glycan, complex, receptor, virus like particle
• Biological source: H-1 parvovirus
• Total number of polymer chains: 60
• Total formula weight: 3785273.34

Authors

Busuttil, K.B.,Bennett, A.B.,McKenna, R. (deposition date: 2025-02-13, release date: 2025-07-23, Last modification date: 2026-02-25)

Primary citation

Busuttil, K.,Pittman, N.,Zachary, J.,Halder, S.,Geilen, L.,Singh, A.,Misseldine, A.,Kaplonek, P.,Chipman, P.,Heimburg-Molinaro, J.,Seeberger, P.H.,Mietzsch, M.,Bennett, A.D.,McKenna, R.
Mapping the sialic acid-binding sites of LuIII and H-1 parvovirus.
J.Virol., 99:e0029725-e0029725, 2025

PubMed Abstract: Oncolytic protoparvoviruses, including LuIII, H-1 parvovirus (H-1PV), and the prototypic strain of minute virus of mice (MVMp), can target and destroy cancer cells. Host cell targeting is based largely on the identification and interaction of the virus with the primary receptor. Previously, it has been shown that MVMp and H-1PV bind to sialic acid (SIA), which is the primary glycan receptor. This study investigates whether LuIII also utilizes a similar glycan for host cell attachment. Microarray analysis confirmed that α2-3-linked SIA is a shared receptor requirement for cell binding for all three viruses. Three glycans were identified in the array, namely, Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAc, Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAc, and Neu5Acα2-3Galβ1-4(Fucα1-3)-GlcNAcβ1-3-Galβ1-4(Fucα1-3)-GlcNAc. The cryo-EM structures of the LuIII and H-1PV glycan complexes were determined to resolutions ranging from 2.57 to 2.88 Å. Small structural perturbations were observed between the cryo-EM map and the previous X-ray crystallographic maps for H-1PV, including several histidine residues within the HI loop. Overall, LuIII and H-1PV utilize a shared SIA recognition pocket near the icosahedral twofold axis adjacent to (but not overlapping with) the known MVMp SIA binding site. In addition, structural differences between the major capsid protein (VP2) of LuIII, H-1PV, and MVMp all clustered around these glycan-binding pockets. This structural phenotype may contribute to the differences observed in tumor cell killing efficiency among the rodent protoparvoviruses.

PubMed: 40704809
DOI: 10.1128/jvi.00297-25

Experimental method

ELECTRON MICROSCOPY (2.57 Å)