6X1I

Two-Component D3 Assembly Constructed by Fusing Symmetric Oligomers to Coiled Coils


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.32 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Geometric Lessons and Design Strategies for Nanoscale Protein Cages.

Laniado, J.Cannon, K.A.Miller, J.E.Sawaya, M.R.McNamara, D.E.Yeates, T.O.

(2021) ACS Nano 15: 4277-4286

  • DOI: https://doi.org/10.1021/acsnano.0c07167
  • Primary Citation of Related Structures:  
    6X1I

  • PubMed Abstract: 

    Protein molecules bring a rich functionality to the field of designed nanoscale architectures. High-symmetry protein cages are rapidly finding diverse applications in biomedicine, nanotechnology, and imaging, but methods for their reliable and predictable construction remain challenging. In this study we introduce an approach for designing protein assemblies that combines ideas and favorable elements adapted from recent work. Cubically symmetric cages can be created by combining two simpler symmetries, following recently established principles. Here, two different oligomeric protein components are brought together in a geometrically specific arrangement by their separate genetic fusion to individual components of a heterodimeric coiled-coil polypeptide motif of known structure. Fusions between components are made by continuous α-helices to limit flexibility. After a computational design, we tested 10 different protein cage constructions experimentally, two of which formed larger assemblies. One produced the intended octahedral cage, ∼26 nm in diameter, while the other appeared to produce the intended tetrahedral cage as a minor component, crystallizing instead in an alternate form representing a collapsed structure of lower stoichiometry and symmetry. Geometric distinctions between the two characterized designs help explain the different degrees of success, leading to clearer principles and improved prospects for the routine creation of nanoscale protein architectures using diverse methods.


  • Organizational Affiliation

    Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cob_adeno_trans domain-containing protein PH0671 fused to a coiled coil172Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0671
UniProt
Find proteins for O58404 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58404 
Go to UniProtKB:  O58404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58404
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SnoaL-like Protein fused to a coiled coil157Agrobacterium fabrum str. C58Mutation(s): 0 
UniProt
Find proteins for Q7D0S4 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7D0S4 
Go to UniProtKB:  Q7D0S4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7D0S4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.32 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.280 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.34α = 90
b = 146.34β = 90
c = 146.34γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1629214

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-04-07
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description