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- PDB-9lzw: Bent-contact of Flock House Virus early disassembly intermediate -

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Basic information

Entry
Database: PDB / ID: 9lzw
TitleBent-contact of Flock House Virus early disassembly intermediate
Components(Capsid protein alpha) x 2
KeywordsVIRUS / Disassembly / Flock House Virus / Asymmetric reconstruction / Single particle reconstruction
Function / homology
Function and homology information


nodavirus endopeptidase / symbiont entry into host cell via permeabilization of host membrane / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Viral coat protein subunit
Similarity search - Domain/homology
Capsid protein alpha
Similarity search - Component
Biological speciesFlock house virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLokshman, M.K. / Kumar, D. / Borkotoky, S. / Banerjee, M.
Funding support India, 1items
OrganizationGrant numberCountry
Other privateFT/288/05/2020 India
CitationJournal: J Mol Biol / Year: 2025
Title: A Disassembly Intermediate of a Non-enveloped Virus Indicates the Pathway of Genome Release.
Authors: Milan Kumar Lokshman / Kirti Suhag / Devbrat Kumar / Subhomoi Borkotoky / Manidipa Banerjee /
Abstract: Disassembly of non-enveloped viruses in vivo are typically triggered by cellular factors such as host receptor binding, low pH in the early or late endosomal compartments, protease action in ...Disassembly of non-enveloped viruses in vivo are typically triggered by cellular factors such as host receptor binding, low pH in the early or late endosomal compartments, protease action in lysosomes, and localized changes in ionic concentrations. These triggers induce alterations in metastable capsids, resulting in the exposure of flexible capsid components and opening of gaps for genome release. Structural analysis of intermediate states is required to understand alterations in protein-protein and RNA-protein contacts in the pathway of capsid destabilization. Obtaining structural details of intermediates requires recreation of the in vivo transition states in stable forms, stepwise, in vitro. Here, we generated an asymmetric reconstruction of an early intermediate state in the disassembly pathway of Flock House Virus, a T = 3 icosahedral insect virus that is a model system for similar-sized non-enveloped viruses. The early intermediate was generated through judicious application, in vitro, of in vivo conditions such as receptor-binding-related transition and endosomal pH. The early intermediate showed asymmetric expansion, as well as asymmetric dynamic movement of the pocket factor, disordering of flexible membrane penetrating peptides and opening of gaps at the 2-fold axis, indicating that disassembly-related structural alterations may be local and not transpire throughout the icosahedral capsid. Surprisingly, the genomic RNA underwent a dramatic conformational alteration which superseded the relatively more subtle changes in the protein component. Recreation of disassembly-related transition states in vitro may be essential for structure-targeted, broadly effective inactivation strategies for non-enveloped viruses.
History
DepositionFeb 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein alpha
D: Capsid protein alpha
B: Capsid protein alpha
E: Capsid protein alpha
C: Capsid protein alpha
F: Capsid protein alpha
G: Capsid protein alpha
J: Capsid protein alpha
H: Capsid protein alpha
K: Capsid protein alpha
I: Capsid protein alpha
L: Capsid protein alpha


Theoretical massNumber of molelcules
Total (without water)262,59812
Polymers262,59812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Segmentation of the asymmetrically reconstructed density map corresponding to two adjacent iASUs at the flat contact (a 2-fold between one 3-fold and adjacent 5-fold ...Evidence: electron microscopy, Segmentation of the asymmetrically reconstructed density map corresponding to two adjacent iASUs at the flat contact (a 2-fold between one 3-fold and adjacent 5-fold axes of symmetry) was performed using Segger. The segmented density was further utilised for map to model building in Phenix providing the crystal structure of FHV (PDB ID: 4FTB) as a reference. The model was further refined against the whole virus map using Coot and Phenix.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Capsid protein alpha


Mass: 39367.355 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Gene: alpha / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P12870, nodavirus endopeptidase
#2: Protein/peptide
Capsid protein alpha


Mass: 4399.056 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Gene: alpha / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P12870, nodavirus endopeptidase
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: Flock House virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Flock House virus
Source (recombinant)Organism: Drosophila melanogaster (fruit fly)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 5.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified wild type FHV particles were treated with low pH and incrementally heated up to 46 degree celcius.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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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 magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 250 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
7Cootmodel fitting
8PHENIXmodel fitting
10cryoSPARC4.4.0initial Euler assignment
11cryoSPARC4.4.0final Euler assignment
13cryoSPARC4.4.03D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 294922
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188205 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215036
ELECTRON MICROSCOPYf_angle_d0.45320550
ELECTRON MICROSCOPYf_dihedral_angle_d4.5822051
ELECTRON MICROSCOPYf_chiral_restr0.0432343
ELECTRON MICROSCOPYf_plane_restr0.0052687

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