3VDX

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains

• PDB DOI: https://doi.org/10.2210/pdb3VDX/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Kitasatospora aureofaciens, Influenza A virus (A/Puerto Rico/8/1934(H1N1))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-06 Released: 2012-06-20 
• Deposition Author(s): Lai, Y.-T., Cascio, D., Yeates, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.281 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Starting Models: experimental

Literature

Structure of a 16-nm cage designed by using protein oligomers.

Lai, Y.T., Cascio, D., Yeates, T.O.

(2012) Science 336: 1129-1129

• PubMed: 22654051 
• DOI: https://doi.org/10.1126/science.1219351
• Primary Citation of Related Structures:  
  3VDX, 4D9J


• PubMed Abstract: 
  

  Designing protein molecules that will assemble into various kinds of ordered materials represents an important challenge in nanotechnology. We report the crystal structure of a 12-subunit protein cage that self-assembles by design to form a tetrahedral structure roughly 16 nanometers in diameter. The strategy of fusing together oligomeric protein domains can be generalized to produce other kinds of cages or extended materials.

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Organizational Affiliation: 

University of California Los Angeles Biomedical Engineering Interdepartmental Program, Los Angeles, CA 90095, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 150.79 kDa 
• Atom Count: 10,149 
• Modelled Residue Count: 1,314 
• Deposited Residue Count: 1,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed 16nm tetrahedral protein cage containing Non-haem bromoperoxidase BPO-A2 and Matrix protein 1	A, B, C	456	Kitasatospora aureofaciens, Influenza A virus (A/Puerto Rico/8/1934(H1N1)) This entity is chimeric	Mutation(s): 0  Gene Names: bpoA2, BROMOPEROXIDASE A2, M, M1 Matrix EC: 1.11.1
UniProt
Find proteins for P29715 (Kitasatospora aureofaciens) Explore P29715  Go to UniProtKB:  P29715
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03485  Go to UniProtKB:  P03485
UniProt Groups	P29715P03485

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.281 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.59	α = 90
b = 127.71	β = 90
c = 204.22	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Lai, Y.-T., Cascio, D., Yeates, T.O.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description