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- PDB-8bi4: Helical shell of CCMV capsid protein on DNA origami 6HB-2k -

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Basic information

Entry
Database: PDB / ID: 8bi4
TitleHelical shell of CCMV capsid protein on DNA origami 6HB-2k
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / origami / capsid
Function / homologyBromovirus coat protein / Bromovirus coat protein / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesCowpea chlorotic mottle virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKumpula, E.-P. / Seitz, I. / Kostiainen, M.A. / Huiskonen, J.T.
Funding supportEuropean Union, Finland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101002258European Union
Academy of Finland341057 Finland
CitationJournal: Nat Nanotechnol / Year: 2023
Title: DNA-origami-directed virus capsid polymorphism.
Authors: Iris Seitz / Sharon Saarinen / Esa-Pekka Kumpula / Donna McNeale / Eduardo Anaya-Plaza / Vili Lampinen / Vesa P Hytönen / Frank Sainsbury / Jeroen J L M Cornelissen / Veikko Linko / Juha T ...Authors: Iris Seitz / Sharon Saarinen / Esa-Pekka Kumpula / Donna McNeale / Eduardo Anaya-Plaza / Vili Lampinen / Vesa P Hytönen / Frank Sainsbury / Jeroen J L M Cornelissen / Veikko Linko / Juha T Huiskonen / Mauri A Kostiainen /
Abstract: Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have ...Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.
History
DepositionNov 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein


Theoretical massNumber of molelcules
Total (without water)122,0186
Polymers122,0186
Non-polymers00
Water0
1
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
x 22


Theoretical massNumber of molelcules
Total (without water)2,684,385132
Polymers2,684,385132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation21

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Components

#1: Protein
Coat protein


Mass: 20336.252 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Cowpea chlorotic mottle virus / References: UniProt: Q548L8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Helical shell of CCMV capsid protein on DNA origami 6HB-2k
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cowpea chlorotic mottle virus
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7ISOLDE1.3model fitting
12cryoSPARC3.3.23D reconstruction
13PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 695465 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial model pdb:1cwp was first manually adjusted to density in ISOLDE and then refined in PHENIX

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