8BI4 | pdb_00008bi4

Helical shell of CCMV capsid protein on DNA origami 6HB-2k

• PDB DOI: https://doi.org/10.2210/pdb8BI4/pdb
• EM Map EMD-16076: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Cowpea chlorotic mottle virus
• Mutation(s): No 


• Deposited: 2022-11-01 Released: 2023-07-05 
• Deposition Author(s): Kumpula, E.-P., Seitz, I., Kostiainen, M.A., Huiskonen, J.T.
• Funding Organization(s): European Research Council (ERC), Academy of Finland

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

DNA-origami-directed virus capsid polymorphism.

Seitz, I., Saarinen, S., Kumpula, E.P., McNeale, D., Anaya-Plaza, E., Lampinen, V., Hytonen, V.P., Sainsbury, F., Cornelissen, J.J.L.M., Linko, V., Huiskonen, J.T., Kostiainen, M.A.

(2023) Nat Nanotechnol 18: 1205-1212

• PubMed: 37460794 
• DOI: https://doi.org/10.1038/s41565-023-01443-x
• Primary Citation Related Structures: 
  8BI4


• PubMed 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 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.

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Organizational Affiliation: 
• Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.
Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, Netherlands.
LIBER Center of Excellence, Aalto University, Aalto, Finland.
Institute of Technology, University of Tartu, Tartu, Estonia.
Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland. [e-mail].
Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland. [e-mail].
LIBER Center of Excellence, Aalto University, Aalto, Finland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 132-mer - A132 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 122.02 kDa 
• Atom Count: 6,600 
• Modeled Residue Count: 882 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A, B, C, D, E, F	190	Cowpea chlorotic mottle virus	Mutation(s): 0
UniProt
Find proteins for P03601 (Cowpea chlorotic mottle virus) Explore P03601  Go to UniProtKB:  P03601

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Kumpula, E.-P., Seitz, I., Kostiainen, M.A., Huiskonen, J.T.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101002258
Academy of Finland	Finland	341057

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references