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- EMDB-36872: Structure of VP9 in Banna virus -

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Basic information

Entry
Database: EMDB / ID: EMD-36872
TitleStructure of VP9 in Banna virus
Map data
Sample
  • Virus: Banna virus
    • Protein or peptide: VP9
Keywordsreceptor binding / spike / reovirus / VIRAL PROTEIN
Function / homologyOuter capsid protein VP9/VP10/VP11 / Outer capsid protein VP9, N-terminal / Reoviridae VP9 / identical protein binding / VP9
Function and homology information
Biological speciesBanna virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi Z / Cao S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0490000 China
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of Banna virus in multiple states reveal stepwise detachment of viral spikes.
Authors: Zhiqiang Li / Han Xia / Guibo Rao / Yan Fu / Tingting Chong / Kexing Tian / Zhiming Yuan / Sheng Cao /
Abstract: Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions- ...Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions-surrounded by 120 spikes (full virions), 60 spikes (partial virions), or no spikes (cores). BAV cores are double-layered particles similar to the cores of other non-turreted reoviruses, except for an additional protein component in the outer capsid shell, VP10. VP10 was identified to be a cementing protein that plays a pivotal role in the assembly of BAV virions by directly interacting with VP2 (inner capsid), VP8 (outer capsid), and VP4 (spike). Viral spikes (VP4/VP9 heterohexamers) are situated on top of VP10 molecules in full or partial virions. Asymmetrical electrostatic interactions between VP10 monomers and VP4 trimers are disrupted by high pH treatment, which is thus a simple way to produce BAV cores. Low pH treatment of BAV virions removes only the flexible receptor binding protein VP9 and triggers significant conformational changes in the membrane penetration protein VP4. BAV virions adopt distinct spatial organization of their surface proteins compared with other well-studied reoviruses, suggesting that BAV may have a unique mechanism of penetration of cellular endomembranes.
History
DepositionJul 17, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36872.png

Downloads & links

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Map

FileDownload / File: emd_36872.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.6747807 - 0.9975674
Average (Standard dev.)0.0017324559 (±0.056755293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 171.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36872_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Banna virus

EntireName: Banna virus
Components
  • Virus: Banna virus
    • Protein or peptide: VP9

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Supramolecule #1: Banna virus

SupramoleculeName: Banna virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 77763 / Sci species name: Banna virus / Sci species strain: YN15-126-01 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP9

MacromoleculeName: VP9 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 30.581178 KDa
SequenceString: MLSETELRAL KKLSTTTSRV VGDSTLALPS NVKLSKGEVE KIAVTKKEMF DELAQCNLPT IELITREHTF NGDVIRFAAW LFLMNGQKL MIANNVAVRM GMQYATNLAG NNVKITYVTS NNVVKLGHIA AGVLANPYSN KGSGLFITYE YNLISNLIET G KVCVLFIT ...String:
MLSETELRAL KKLSTTTSRV VGDSTLALPS NVKLSKGEVE KIAVTKKEMF DELAQCNLPT IELITREHTF NGDVIRFAAW LFLMNGQKL MIANNVAVRM GMQYATNLAG NNVKITYVTS NNVVKLGHIA AGVLANPYSN KGSGLFITYE YNLISNLIET G KVCVLFIT SLSTTASSTN SFAYSTCSVP IENWDFNMIK LTAETSCASL TAMTNLVNSL VPGERTRPVG LYVDIPGVTV TT SASSGSL PLTTIPAVTP LIFSAYTKQV EEVGVINTLY ALSYLP

UniProtKB: VP9

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 443253
FSC plot (resolution estimation)

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