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- EMDB-6936: Cryo-EM reconstruction of flexible nanotubes self-assembled from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6936
TitleCryo-EM reconstruction of flexible nanotubes self-assembled from baculovirus major capsid protein
Map data
Sample
  • Virus: Helicoverpa armigera nucleopolyhedrovirus
Biological speciesHelicoverpa armigera nucleopolyhedrovirus
Methodhelical reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsRao G / Fu Y / Li N / Yin J / Zhang J / Wang M / Hu Z / Cao S
CitationJournal: ACS Appl Mater Interfaces / Year: 2018
Title: Controllable Assembly of Flexible Protein Nanotubes for Loading Multifunctional Modules.
Authors: Guibo Rao / Yan Fu / Na Li / Jiayi Yin / Jie Zhang / Manli Wang / Zhihong Hu / Sheng Cao /
Abstract: Viruses with filamentous morphologies, such as tobacco mosaic virus (TMV) and M13 bacteriophage, have long been studied as multivalent nanoscaffolds for loading functional motifs. Structural assembly ...Viruses with filamentous morphologies, such as tobacco mosaic virus (TMV) and M13 bacteriophage, have long been studied as multivalent nanoscaffolds for loading functional motifs. Structural assembly of the capsid proteins (CPs) of filamentous viruses often requires the presence of DNA or RNA molecules, which has limited their applications. Here, we describe a strategy for controllable assembly of flexible bio-nanotubes consisting of Escherichia coli expressed CP of baculovirus Helicoverpa armigera nucleopolyhedrovirus (HearNPV) in vitro. These protein-only nanotubes were studied as a new structural platform for high-density presentation of multiple active molecules on the exterior surface by direct fusion of the protein of interest to the N-terminus of HearNPV CP (HaCP). Structural characterization using cryoelectron microscopy demonstrated that the HaCP could assemble into two closely related but structurally distinct tube types, suggesting the tunable HaCP interaction network is the major contributor to the flexibility of HaCP nanotubes. Our flexible nanotubes could tolerate larger molecular modifications compared with TMV-based templates and could be used as promising candidates for versatile molecular loading applications.
History
DepositionApr 10, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseAug 29, 2018-
UpdateAug 29, 2018-
Current statusAug 29, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0094
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0094
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6936.png

Downloads & links

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Map

FileDownload / File: emd_6936.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 400 pix.
= 405.6 Å		1.01 Å/pix.
x 400 pix.
= 405.6 Å		1.01 Å/pix.
x 400 pix.
= 405.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0094 / Movie #1: 0.0094
Minimum - Maximum-0.003443933 - 0.014832972
Average (Standard dev.)0.0009719717 (±0.0029214784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 405.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z405.600405.600405.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0030.0150.001

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Supplemental data

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Sample components

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Entire : Helicoverpa armigera nucleopolyhedrovirus

EntireName: Helicoverpa armigera nucleopolyhedrovirus
Components
  • Virus: Helicoverpa armigera nucleopolyhedrovirus

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Supramolecule #1: Helicoverpa armigera nucleopolyhedrovirus

SupramoleculeName: Helicoverpa armigera nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 51313 / Sci species name: Helicoverpa armigera nucleopolyhedrovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli (E. coli)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 34.74 Å
Applied symmetry - Helical parameters - Δ&Phi: 11.25 °
Applied symmetry - Helical parameters - Axial symmetry: C12 (12 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 551
Final angle assignmentType: NOT APPLICABLE

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