9DND | pdb_00009dnd

Pseudosymmetric protein nanocage GI4 -F7 (local refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hierarchical design of pseudosymmetric protein nanocages.

Dowling, Q.M.Park, Y.J.Fries, C.N.Gerstenmaier, N.C.Ols, S.Yang, E.C.Wargacki, A.J.Dosey, A.Hsia, Y.Ravichandran, R.Walkey, C.D.Burrell, A.L.Veesler, D.Baker, D.King, N.P.

(2025) Nature 638: 553-561

  • DOI: https://doi.org/10.1038/s41586-024-08360-6
  • Primary Citation of Related Structures:  
    9DND, 9DNE

  • PubMed Abstract: 

    Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions 1,2 . Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry 3 . Here, inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540 and 960 subunits. At 49, 71 and 96 nm diameter, these nanocages are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work substantially broadens the variety of self-assembling protein architectures that are accessible through design.


  • Organizational Affiliation
    • Department of Bioengineering, University of Washington, Seattle, WA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudosymmetric protein nanocages GI4 A ChainA [auth D],
C [auth A]
225synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudosymmetric protein nanocages GI4 C ChainB [auth C]215synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pseudosymmetric protein nanocages GI4 B ChainD [auth B]205synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI158186

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Data collection, Database references
  • Version 1.2: 2025-02-26
    Changes: Data collection, Database references