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- EMDB-53718: Hexahistidine-tagged tobacco mosaic virus coat protein 5-layer disk -

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Basic information

Entry
Database: EMDB / ID: EMD-53718
TitleHexahistidine-tagged tobacco mosaic virus coat protein 5-layer disk
Map datamain map
Sample
  • Complex: 5-layer TMV disk
    • Protein or peptide: tobacco mosaic virus coat protein
KeywordsTMV / coat protein / supramolecular assembly / STRUCTURAL PROTEIN
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsBiela AP / Abu-Baker I
Funding support Canada, 3 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT) Canada
Canada Foundation for Innovation Canada
CitationJournal: Small / Year: 2025
Title: Extended Plasmonic Nanostructures Templated by Tobacco Mosaic Virus Coat Protein.
Authors: Ismael Abu-Baker / Alexander Al-Feghali / Elliot Zolfaghar / Gangamallaiah Velpula / Artur P Biela / Steven De Feyter / Jonathan G Heddle / Gonzalo Cosa / Amy Szuchmacher Blum /
Abstract: Optical and magnetic metamaterials possess interesting properties that cannot be achieved with conventional materials. However, there is currently no synthetic method offering both scalability and ...Optical and magnetic metamaterials possess interesting properties that cannot be achieved with conventional materials. However, there is currently no synthetic method offering both scalability and nanometer spatial precision. Biotemplating is a promising technique that has the potential to organize nanoscale components with high precision while being scalable and low-cost. Here, we demonstrate a versatile template using hexahistidine-tagged tobacco mosaic virus coat protein. The protein self-assembles into disks, which further assemble into extended nanostructures under mild conditions. Large sheets with either hexagonal or square packing and core-shell nanorods are formed, and gold nanoparticles are attached to the disks within each nanostructure to form assemblies of nanoparticle rings.
History
DepositionMay 14, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53718.png

Downloads & links

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Map

FileDownload / File: emd_53718.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 450 pix.
= 378. Å		0.84 Å/pix.
x 450 pix.
= 378. Å		0.84 Å/pix.
x 450 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.091
Minimum - Maximum-0.17078723 - 0.23698232
Average (Standard dev.)0.0022889497 (±0.017999563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_53718_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_53718_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 5-layer TMV disk

EntireName: 5-layer TMV disk
Components
  • Complex: 5-layer TMV disk
    • Protein or peptide: tobacco mosaic virus coat protein

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Supramolecule #1: 5-layer TMV disk

SupramoleculeName: 5-layer TMV disk / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nicotiana tabacum (common tobacco)

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Macromolecule #1: tobacco mosaic virus coat protein

MacromoleculeName: tobacco mosaic virus coat protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
MSYSITTPSQ FVFLSSAWAD PIELINLCTN ALGNQFQTQQ ARTVVQRQFS EVWKPSPQVT VRFPDSDFKV YRYNAVLDPL VTALLGAFDT RNRIIEVENQ ANPTTAETLD ATRRVDDATV AIRSAINNLI VELIRGTGSY NRSSFESSSG LVWTSGPATH HHHHH

UniProtKB: Capsid protein

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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: 6
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8488 / 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: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3400 / Details: auto-picked particles
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C17 (17 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2598
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Avg.num./class: 20000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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