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- PDB-8w9r: Structure of Banna virus core -

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Basic information

Entry
Database: PDB / ID: 8w9r
TitleStructure of Banna virus core
Components
  • VP10VP9
  • VP8
  • Vp2
KeywordsVIRUS / core particle / capsid protein / reovirus / complex
Function / homologyStructural protein Vp10, Seadornavirus / Seadornavirus VP8 protein / Seadornavirus Vp10 / Seadornavirus VP2 protein / VP10 / Vp2 / VP8
Function and homology information
Biological speciesBanna virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLi, Z. / Cao, S.
Funding support China, 1items
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
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vp2
B: Vp2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10


Theoretical massNumber of molelcules
Total (without water)700,88317
Polymers700,88317
Non-polymers00
Water0
1
A: Vp2
B: Vp2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
x 60


Theoretical massNumber of molelcules
Total (without water)42,052,9511020
Polymers42,052,9511020
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: Vp2
B: Vp2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
x 5


  • icosahedral pentamer
  • 3.5 MDa, 85 polymers
Theoretical massNumber of molelcules
Total (without water)3,504,41385
Polymers3,504,41385
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Vp2
B: Vp2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
x 6


  • icosahedral 23 hexamer
  • 4.21 MDa, 102 polymers
Theoretical massNumber of molelcules
Total (without water)4,205,295102
Polymers4,205,295102
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 Vp2


Mass: 108031.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OR004519 / Source: (natural) Banna virus / References: UniProt: Q9INH3
#2: Protein
VP8


Mass: 32885.305 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Details: OR004525 / Source: (natural) Banna virus / References: UniProt: W0G587
#3: Protein VP10 / VP9


Mass: 28655.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OR004527 / Source: (natural) Banna virus / References: UniProt: A0A2H4QDD3

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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: Banna virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Banna virus / Strain: YN15-126-01
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42352 / Symmetry type: POINT

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