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- PDB-8y3n: The self-assembled nanotube of CPC46A/Q70C -

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Basic information

Entry
Database: PDB / ID: 8y3n
TitleThe self-assembled nanotube of CPC46A/Q70C
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Capsid protein / Self-assembly / Nanotube
Function / homologyLevivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesEmesvirus zinderi
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang, M. / Rao, G. / Li, L. / Qi, L. / Ma, C. / Zhang, H. / Gong, J. / Wei, B. / Zhang, X.E. / Chen, G. ...Yang, M. / Rao, G. / Li, L. / Qi, L. / Ma, C. / Zhang, H. / Gong, J. / Wei, B. / Zhang, X.E. / Chen, G. / Cao, S. / Li, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22293033 China
Other government2022YFC2303502
Other government2022020801010146
CitationJournal: ACS Nano / Year: 2024
Title: Transformation of a Viral Capsid from Nanocages to Nanotubes and Then to Hydrogels: Redirected Self-Assembly and Effects on Immunogenicity.
Authors: Mengsi Yang / Guibo Rao / Long Li / Linlin Qi / Chun Ma / Hui Zhang / Jun Gong / Bin Wei / Xian-En Zhang / Guosong Chen / Sheng Cao / Feng Li /
Abstract: The ability to manipulate the self-assembly of proteins is essential to understanding the mechanisms of life and beneficial to fabricating advanced nanomaterials. Here, we report the transformation ...The ability to manipulate the self-assembly of proteins is essential to understanding the mechanisms of life and beneficial to fabricating advanced nanomaterials. Here, we report the transformation of the MS2 phage capsid from nanocages to nanotubes and then to nanotube hydrogels through simple point mutations guided by interfacial interaction redesign. We demonstrate that site 70, which lies in the flexible FG loop of the capsid protein (CP), is a "magic" site that can largely dictate the final morphology of assemblies. By varying the amino acid at site 70, with the aid of a cysteine-to-alanine mutation at site 46, we achieved the assembly of double-helical or single-helical nanotubes in addition to nanocages. Furthermore, an additional cysteine substitution on the surface of nanotubes mediated their cross-linking to form hydrogels with reducing agent responsiveness. The hierarchical self-assembly system allowed for the investigation of morphology-related immunogenicity of MS2 CPs, which revealed dramatic differences among nanocages, nanotubes, and nanotube hydrogels in terms of immune response types, antibody levels and T cell functions. This study provides insights into the assembly manipulation of protein nanomaterials and the customized design of nanovaccines and drug delivery systems.
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)54,7264
Polymers54,7264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Capsid protein / Coat protein


Mass: 13681.413 Da / Num. of mol.: 4 / Mutation: C47A, Q71C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emesvirus zinderi / Gene: cp / Production host: Escherichia coli (E. coli) / References: UniProt: C8XPD7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: CPC46A/Q70C / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Emesvirus zinderi
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 104.141 ° / Axial rise/subunit: 27.464 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 564085 / Symmetry type: HELICAL

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