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- PDB-11ov: Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03 -

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Basic information

Entry
Database: PDB / ID: 11ov
TitleCryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03
Components
  • 5H03 Fab heavy chain
  • 5H03 Fab light chain
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS LIKE PARTICLE / EV-D68 / B3 subclade / 5H03 neutralizing antibody
Function / homology
Function and homology information


picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / virion component / ribonucleoside triphosphate phosphatase activity / host cell / nucleoside-triphosphate phosphatase ...picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / virion component / ribonucleoside triphosphate phosphatase activity / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...: / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus D68
Macaca mulatta (Rhesus monkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsCheng, J. / Lei, H. / Pletnev, S. / Morano, N.C. / Zhang, B. / Du, H. / Rubin, S. / Moss, D.L. / Krug, P.W. / Kanekiyo, M. ...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. / Shapiro, L. / Kwong, P.D. / Zhou, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Transl Med / Year: 2026
Title: Neutralizing antibodies elicited in nonhuman primates by an enterovirus D68 virus-like particle vaccine target receptor binding sites.
Authors: Daniel L Moss / Jiaxuan Cheng / Peter W Krug / Alden C Paine / Brian E Fisher / Amy R Henry / Jesmine Roberts-Torres / Timothy S Johnston / Sarah C Smith / Sergei Pletnev / Haotian Lei / ...Authors: Daniel L Moss / Jiaxuan Cheng / Peter W Krug / Alden C Paine / Brian E Fisher / Amy R Henry / Jesmine Roberts-Torres / Timothy S Johnston / Sarah C Smith / Sergei Pletnev / Haotian Lei / Nicholas C Morano / Theodore C Pierson / Lawrence Shapiro / Tongqing Zhou / Peter D Kwong / Daniel C Douek / Masaru Kanekiyo / Tracy J Ruckwardt /
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 ...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.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
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Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
h: 5H03 Fab heavy chain
l: 5H03 Fab light chain


Theoretical massNumber of molelcules
Total (without water)102,2365
Polymers102,2365
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Capsid protein VP1


Mass: 25735.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68 / Production host: Homo sapiens (human) / References: UniProt: A0A7G9XUH9
#2: Protein Capsid protein VP0


Mass: 23797.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68 / Production host: Homo sapiens (human)
References: UniProt: A0A5B9NIG2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Capsid protein VP3


Mass: 27170.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68 / Production host: Homo sapiens (human)
References: UniProt: A0A1L7H9D2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Antibody 5H03 Fab heavy chain


Mass: 13768.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#5: Antibody 5H03 Fab light chain


Mass: 11764.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human enterovirus D68
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SUBSPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.5 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48000 / Symmetry type: POINT
RefinementHighest resolution: 2.83 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057161
ELECTRON MICROSCOPYf_angle_d1.2029742
ELECTRON MICROSCOPYf_dihedral_angle_d5.892962
ELECTRON MICROSCOPYf_chiral_restr0.0541081
ELECTRON MICROSCOPYf_plane_restr0.0081249

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