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- PDB-9dog: Octahedral small virus-like particles of dengue virus type 2 (oct... -

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Basic information

Entry
Database: PDB / ID: 9dog
TitleOctahedral small virus-like particles of dengue virus type 2 (octahedral reconstruction)
Components
  • Protein prM
  • glycoprotein E
KeywordsVIRUS LIKE PARTICLE / dengue virus type 2 / virus / flavivirus / virus-like particle / prM-E protein / fusion protein / cryoEM
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 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
Similarity search - Component
Biological speciesdengue virus type 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsJohnson, A. / Dodes Traian, M. / Walsh, R.M. / Jenni, S. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J Virol / Year: 2025
Title: Octahedral small virus-like particles of dengue virus type 2.
Authors: Adam Johnson / Martín Dodes Traian / Richard M Walsh / Simon Jenni / Stephen C Harrison /
Abstract: Flavivirus envelope (E) and precursor M (prM) proteins, when ectopically expressed, assemble into empty, virus-like particles (VLPs). Cleavage of prM to M and loss of the pr fragment converts the ...Flavivirus envelope (E) and precursor M (prM) proteins, when ectopically expressed, assemble into empty, virus-like particles (VLPs). Cleavage of prM to M and loss of the pr fragment converts the VLPs from immature to mature particles, mimicking a similar maturation of authentic virions. Most of the VLPs obtained by prM-E expression are smaller than virions; early, low-resolution cryo-EM studies suggested a simple, 60-subunit, icosahedral organization. We describe here the cryo-EM structure of immature, small VLPs (smVLPs) from dengue virus type 2 and show that they have octahedral rather than icosahedral symmetry. The asymmetric unit of the octahedral particle is an asymmetric trimer of prM-E heterodimers, just as it is on icosahedral immature virions; the full, octahedrally symmetric particle thus has 24 such asymmetric trimers or 72 prM-E heterodimers in all. Cleavage of prM and release of pr generates ovoid, somewhat irregular, mature particles. Previous work has shown that mature smVLPs have fusion properties identical to those of virions, consistent with local, virion-like clustering of 36 E dimers on their surface. The cryo-EM structure and the properties of the smVLPs described here relate directly to ongoing efforts to use them as vaccine immunogens.
IMPORTANCE: Ectopic expression of flavivirus envelope (E) and precursor M (prM) proteins leads to the formation and secretion of empty, virus-like particles (VLPs). We show that a major class of ...IMPORTANCE: Ectopic expression of flavivirus envelope (E) and precursor M (prM) proteins leads to the formation and secretion of empty, virus-like particles (VLPs). We show that a major class of VLPs, of smaller diameter than those of virion size ("small VLPs": smVLPs), are octahedrally symmetric particles. The known characteristics of immature virions (asymmetric trimers of prM-E heterodimers) allow us to understand the assembly of an octahedral (rather than icosahedral) surface lattice. Cleavage of prM and formation of mature, fusogenic smVLPs yield somewhat irregular, ovoid particles. These observations are directly relevant to proposals for using immunogenic but non-infectious VLPs as components of specific flavivirus vaccines.
History
DepositionSep 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _em_admin.last_update
Revision 1.2Mar 12, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A000: glycoprotein E
C004: glycoprotein E
D004: Protein prM
E004: Protein prM
F004: Protein prM
A005: glycoprotein E
B005: glycoprotein E
C005: glycoprotein E
D005: Protein prM
E005: Protein prM
F005: Protein prM
A006: glycoprotein E
B006: glycoprotein E
C006: glycoprotein E
D006: Protein prM
E006: Protein prM
F006: Protein prM
A007: glycoprotein E
B007: glycoprotein E
C007: glycoprotein E
D007: Protein prM
E007: Protein prM
F007: Protein prM
A008: glycoprotein E
B008: glycoprotein E
C008: glycoprotein E
D008: Protein prM
B000: glycoprotein E
E008: Protein prM
F008: Protein prM
A009: glycoprotein E
B009: glycoprotein E
C009: glycoprotein E
D009: Protein prM
E009: Protein prM
F009: Protein prM
A010: glycoprotein E
B010: glycoprotein E
C010: glycoprotein E
D010: Protein prM
E010: Protein prM
F010: Protein prM
A011: glycoprotein E
B011: glycoprotein E
C011: glycoprotein E
D011: Protein prM
E011: Protein prM
F011: Protein prM
A012: glycoprotein E
B012: glycoprotein E
C012: glycoprotein E
D012: Protein prM
E012: Protein prM
F012: Protein prM
C000: glycoprotein E
A013: glycoprotein E
B013: glycoprotein E
C013: glycoprotein E
D013: Protein prM
E013: Protein prM
F013: Protein prM
A014: glycoprotein E
B014: glycoprotein E
C014: glycoprotein E
D014: Protein prM
E014: Protein prM
F014: Protein prM
A015: glycoprotein E
B015: glycoprotein E
C015: glycoprotein E
D015: Protein prM
E015: Protein prM
F015: Protein prM
A016: glycoprotein E
B016: glycoprotein E
C016: glycoprotein E
D016: Protein prM
E016: Protein prM
F016: Protein prM
A017: glycoprotein E
B017: glycoprotein E
D000: Protein prM
C017: glycoprotein E
D017: Protein prM
E017: Protein prM
F017: Protein prM
A018: glycoprotein E
B018: glycoprotein E
C018: glycoprotein E
D018: Protein prM
E018: Protein prM
F018: Protein prM
A019: glycoprotein E
B019: glycoprotein E
C019: glycoprotein E
D019: Protein prM
E019: Protein prM
F019: Protein prM
A020: glycoprotein E
B020: glycoprotein E
C020: glycoprotein E
D020: Protein prM
E020: Protein prM
F020: Protein prM
A021: glycoprotein E
B021: glycoprotein E
C021: glycoprotein E
D021: Protein prM
E000: Protein prM
E021: Protein prM
F021: Protein prM
A022: glycoprotein E
B022: glycoprotein E
C022: glycoprotein E
D022: Protein prM
E022: Protein prM
F022: Protein prM
A023: glycoprotein E
B023: glycoprotein E
C023: glycoprotein E
D023: Protein prM
E023: Protein prM
F023: Protein prM
F000: Protein prM
A001: glycoprotein E
B001: glycoprotein E
C001: glycoprotein E
D001: Protein prM
E001: Protein prM
F001: Protein prM
A002: glycoprotein E
B002: glycoprotein E
C002: glycoprotein E
D002: Protein prM
E002: Protein prM
F002: Protein prM
A003: glycoprotein E
B003: glycoprotein E
C003: glycoprotein E
D003: Protein prM
E003: Protein prM
F003: Protein prM
A004: glycoprotein E
B004: glycoprotein E


  • 5.27 MDa, 144 polymers
  • Cα atoms only: ...Cα atoms only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
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)5,271,516144
Polymers5,271,516144
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
glycoprotein E / Coordinate model: Cα atoms only


Mass: 54363.801 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: G3GAJ4
#2: Protein ...
Protein prM / Coordinate model: Cα atoms only


Mass: 18851.695 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P14340
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: dengue virus type 2 / Type: VIRUS / Details: Octahedral reconstruction / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: dengue virus type 2
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 42.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38934 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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