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- EMDB-38898: The self-assembled nanotube of CPC46A/Q70H -

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Basic information

Entry
Database: EMDB / ID: EMD-38898
TitleThe self-assembled nanotube of CPC46A/Q70H
Map dataEM map
Sample
  • Complex: CPC46A/Q70H
    • Protein or peptide: Capsid protein
KeywordsCapsid protein / Self-assembly / Nanotube / VIRAL PROTEIN
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
Methodhelical reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsYang M / Rao G / Li L / Qi L / Ma C / Zhang H / Gong J / Wei B / Zhang XE / Chen G ...Yang M / Rao G / Li L / Qi L / Ma C / Zhang H / Gong J / Wei B / Zhang XE / Chen G / Cao S / Li F
Funding support China, 3 items
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, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38898.png

Downloads & links

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Map

FileDownload / File: emd_38898.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2267817 - 1.9195137
Average (Standard dev.)0.004374383 (±0.09086906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map

Fileemd_38898_half_map_1.map
AnnotationEM half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map

Fileemd_38898_half_map_2.map
AnnotationEM half 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 : CPC46A/Q70H

EntireName: CPC46A/Q70H
Components
  • Complex: CPC46A/Q70H
    • Protein or peptide: Capsid protein

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Supramolecule #1: CPC46A/Q70H

SupramoleculeName: CPC46A/Q70H / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Emesvirus zinderi

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Emesvirus zinderi
Molecular weightTheoretical: 13.716417 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ASNFTQFVLV DNGGTGDVTV APSNFANGVA EWISSNSRSQ AYKVTASVRQ SSAQNRKYTI KVEVPKVATH TVGGVELPVA AWRSYLNME LTIPIFATNS DCELIVKAMQ GLLKDGNPIP SAIAANSGIY

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.137 Å
Applied symmetry - Helical parameters - Δ&Phi: 102.047 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4560458
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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