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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 / DNA-templated transcription / virion attachment to host cell / host cell nucleus / 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: To Be Published
Title: Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03
Authors: 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.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary 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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