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- PDB-9c8g: Cryo-EM Structure of EV-D68 A2 Inactivated Virus Particle -

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Basic information

Entry
Database: PDB / ID: 9c8g
TitleCryo-EM Structure of EV-D68 A2 Inactivated Virus Particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS LIKE PARTICLE / EV-D68 / B3 subclade / VLP
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host NF-kappaB cascade / 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 / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm
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 (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 / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsCheng, J. / Krug, P.W. / Lei, H. / Moss, D.L. / Huang, R. / Lang, Z.C. / Morton, A.J. / Shen, C. / Pierson, T.C. / Zhou, T. ...Cheng, J. / Krug, P.W. / Lei, H. / Moss, D.L. / Huang, R. / Lang, Z.C. / Morton, A.J. / Shen, C. / Pierson, T.C. / Zhou, T. / Ruckwardt, T.J. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights from vaccine candidates for EV-D68.
Authors: Jiaxuan Cheng / Peter W Krug / Haotian Lei / Daniel L Moss / Zabrina C Lang / Abraham J Morton / Chen-Hsiang Shen / Sergei Pletnev / Rick K Huang / Theodore C Pierson / Tongqing Zhou / Tracy ...Authors: Jiaxuan Cheng / Peter W Krug / Haotian Lei / Daniel L Moss / Zabrina C Lang / Abraham J Morton / Chen-Hsiang Shen / Sergei Pletnev / Rick K Huang / Theodore C Pierson / Tongqing Zhou / Tracy J Ruckwardt / Peter D Kwong /
Abstract: Enterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we ...Enterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we determine cryo-EM structures of EV-D68 virus-like particles (VLPs), inactivated virus particles (InVPs), and altered virus particles (A-particles) from B3 and A2 subclades. The B3 VLP is a current vaccine candidate, which we show closely resembles its InVP counterpart, particularly at the 5-fold axis of symmetry, the target of potent neutralizing antibodies. Similar structural conservation was observed in the A2 subclade. Sequence variation between B3 and A2 mainly occurred in flexible loops displayed on the particle surface. A canyon-filling pocket factor was present in B3 InVP but absent in A2 InVP. A-particles were predominant in β-propiolactone-inactivated virus at longer but not shorter incubation. Overall, our findings highlight EV-D68 similarities and subclade-specific differences, offering structural insights that relate to vaccine development.
History
DepositionJun 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4


Theoretical massNumber of molelcules
Total (without water)95,3314
Polymers95,3314
Non-polymers00
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,719,853240
Polymers5,719,853240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP2
C: VP3
D: VP4
x 5


  • icosahedral pentamer
  • 477 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)476,65420
Polymers476,65420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
x 6


  • icosahedral 23 hexamer
  • 572 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)571,98524
Polymers571,98524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1


Mass: 32956.465 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: A0A8D5ZMD3
#2: Protein VP2


Mass: 27624.227 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: A0A286KB20
#3: Protein VP3


Mass: 27282.035 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: A0A097BW19
#4: Protein VP4


Mass: 7468.157 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: Q68T42
Has protein modificationN

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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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066482
ELECTRON MICROSCOPYf_angle_d1.1288835
ELECTRON MICROSCOPYf_dihedral_angle_d6.443860
ELECTRON MICROSCOPYf_chiral_restr0.063994
ELECTRON MICROSCOPYf_plane_restr0.0091143

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