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- EMDB-63529: Early disassembly intermediate of Flock House Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-63529
TitleEarly disassembly intermediate of Flock House Virus
Map data
Sample
  • Virus: Flock House virus
    • Protein or peptide: Capsid protein alpha
    • Protein or peptide: Capsid protein alpha
KeywordsDisassembly / Flock House Virus / Asymmetric reconstruction / Single Particle Reconstruction / VIRUS
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 / Flock House virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLokshman MK / Kumar D / Borkotoky S / Banerjee M
Funding support India, 1 items
OrganizationGrant numberCountry
Other privateFT/5/288/2020 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, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_63529.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å
1.1 Å/pix.
x 480 pix.
= 528. Å
1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.7802636 - 1.4023869
Average (Standard dev.)0.0073991814 (±0.08168853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63529_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_63529_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_63529_half_map_2.map
Projections & Slices
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Sample components

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Entire : Flock House virus

EntireName: Flock House virus
Components
  • Virus: Flock House virus
    • Protein or peptide: Capsid protein alpha
    • Protein or peptide: Capsid protein alpha

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Supramolecule #1: Flock House virus

SupramoleculeName: Flock House virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12287 / Sci species name: Flock House virus / Virus type: VIROID / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein alpha

MacromoleculeName: Capsid protein alpha / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: nodavirus endopeptidase
Source (natural)Organism: Flock house virus
Molecular weightTheoretical: 39.367355 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MVNNNRPRRQ RAQRVVVTTT QTAPVPQQNV PRNGRRRRNR TRRNRRRVRG MNMAALTRLS QPGLAFLKCA FAPPDFNTDP GKGIPDRFE GKVVSRKDVL NQSISFTAGQ DTFILIAPTP GVAYWSASVP AGTFPTSATT FNPVNYPGFT SMFGTTSTSR S DQVSSFRY ...String:
MVNNNRPRRQ RAQRVVVTTT QTAPVPQQNV PRNGRRRRNR TRRNRRRVRG MNMAALTRLS QPGLAFLKCA FAPPDFNTDP GKGIPDRFE GKVVSRKDVL NQSISFTAGQ DTFILIAPTP GVAYWSASVP AGTFPTSATT FNPVNYPGFT SMFGTTSTSR S DQVSSFRY ASMNVGIYPT SNLMQFAGSI TVWKCPVKLS TVQFPVATDP ATSSLVHTLV GLDGVLAVGP DNFSESFIKG VF SQSACNE PDFEFNDILE GIQTLPPANV SLGSTGQPFT MDSGAEATSG VVGWGNMDTI VIRVSAPEGA VNSAILKAWS CIE YRPNPN AMLYQFGHDS PPLDEVALQE YRTVARSLPV AVIAAQN

UniProtKB: Capsid protein alpha

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Macromolecule #2: Capsid protein alpha

MacromoleculeName: Capsid protein alpha / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: nodavirus endopeptidase
Source (natural)Organism: Flock house virus
Molecular weightTheoretical: 4.399056 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
ASMWERVKSI IKSSLAAASN IPGPIGVAAS GISGLSALFE GFGF

UniProtKB: Capsid protein alpha

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 5.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified wild type FHV particles were treated with low pH and incrementally heated up to 46 degree celcius.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 188205
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9lzl:
Flat-contact of Flock House Virus early disassembly intermediate

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

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