11LT | pdb_000011lt

Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 1E11

PDB DOI: https://doi.org/10.2210/pdb11LT/pdb
EM Map EMD-75818: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): enterovirus D68, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-03-03 Released: 2026-05-27
Deposition Author(s): Cheng, J., Lei, H., Pletnev, S., Morano, N.C., Zhang, B., Du, H., Rubin, S., Moss, D.L., Krug, P.W., Kanekiyo, M., Pierson, T.C., Ruckwardt, T.J., Kwong, P.D., Zhou, T.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Neutralizing antibodies elicited in nonhuman primates by an enterovirus D68 virus-like particle vaccine target receptor binding sites.

Moss, D.L., Cheng, J., Krug, P.W., Paine, A.C., Fisher, B.E., Henry, A.R., Roberts-Torres, J., Johnston, T.S., Smith, S.C., Pletnev, S., Lei, H., Morano, N.C., Pierson, T.C., Shapiro, L., Zhou, T., Kwong, P.D., Douek, D.C., Kanekiyo, M., Ruckwardt, T.J.

(2026) Sci Transl Med 18: eaec5446-eaec5446

PubMed: 42234771 Search on PubMed
DOI: https://doi.org/10.1126/scitranslmed.aec5446
Primary Citation Related Structures:
11LT, 11OV

PubMed Abstract:
Enterovirus D68 (EV-D68) is a picornavirus that causes biennial outbreaks of respiratory disease in young children that can progress to rare but severe complications, including acute flaccid myelitis (AFM). EV-D68 virus-like particles (VLPs) elicit potent neutralizing antibodies that are protective in animal models. Here, we report the isolation and characterization of monoclonal antibodies elicited by EV-D68 VLPs in nonhuman primates (NHPs). We identified five potently neutralizing mAbs targeting overlapping epitopes near the capsid fivefold axis of symmetry formed by pentamers of viral protein 1. Cryo-electron microscopy structures of mAbs 1E11 and 5H03 in complex with VLP revealed epitopes on the capsid that bridge the sialic acid binding site and the proteinaceous entry receptor major facilitator superfamily domain-containing protein 6 binding site. We further characterized the mechanisms by which these mAbs neutralize EV-D68 and found that mAbs can disrupt multiple steps in the EV-D68 life cycle, including promoting premature uncoating. Antibodies elicited by VLP immunization of NHP protected as well as a best-in-class human mAb in a mouse challenge model, although single-amino acid mutations in the capsid enabled viral escape. Our results demonstrate that EV-D68 VLP-elicited mAbs target major viral sites of vulnerability, provide insight into their mechanisms of neutralization, and reinforce the potential for VLP-based vaccines as a countermeasure for EV-D68.

Organizational Affiliation

Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 102.39 kDa
Atom Count: 7,004
Modeled Residue Count: 895
Deposited Residue Count: 921
Unique protein chains: 5

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	229	enterovirus D68	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP0	B	212	enterovirus D68	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C	247	enterovirus D68	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)