Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 28764.82 
• Atom Count: 1993 
• Residue Count: 248 
• Unique protein chains: 1

5YRD

Crystal Structure of Oxidized Cypovirus Polyhedra R13A/S193C/A194C Mutant

• DOI: 10.2210/pdb5YRD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bombyx mori cytoplasmic polyhedrosis virus
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


• Deposited: 2017-11-09 Released: 2018-02-21 
• Deposition Author(s): Negishi, H., Abe, S., Yamashita, K., Hirata, K., Niwase, K., Boudes, M., Coulibaly, F., Mori, H., Ueno, T.
• Funding Organization(s): JSPS 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.222 
• R-Value Work: 0.162 

Literature

Supramolecular protein cages constructed from a crystalline protein matrix

Negishi, H., Abe, S., Yamashita, K., Hirata, K., Niwase, K., Boudes, M., Coulibaly, F., Mori, H., Ueno, T.

(2018) Chem. Commun. (Camb.) 54: 1988-1991

• PubMed: 29405208 
• DOI: 10.1039/c7cc08689j
• Primary Citation of Related Structures:  
  5YRC, 5YRB, 5YRA, 5YR9, 5YR1


• PubMed Abstract: 
  

Protein crystals are formed via ordered arrangements of proteins, which assemble to form supramolecular structures. Here, we show a method for the assembly of supramolecular protein cages within a crystalline environment. The cages are stabilized by covalent cross-linking allowing their release via dissolution of the crystal. The high stability of the desiccated protein crystals allows cages to be constructed.

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Organizational Affiliation: 

School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. [e-mail] [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Polyhedrin	A	248	Bombyx mori cytoplasmic polyhedrosis virus	Mutation(s): 3
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus) Go to UniProtKB:  P11041

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.222 
• R-Value Work: 0.162 
• Space Group: I 2 3

Unit Cell:

Length (Å)	Angle (°)
a = 103.620	α = 90.00
b = 103.620	β = 90.00
c = 103.620	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PHENIX	phasing
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-09 
• Released Date: 2018-02-21 
• Deposition Author(s): Negishi, H., Abe, S., Yamashita, K., Hirata, K., Niwase, K., Boudes, M., Coulibaly, F., Mori, H., Ueno, T.

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Funding Organization	Location	Grant Number
JSPS	Japan	26620130
JSPS	Japan	15J11955

Revision History 

• Version 1.0: 2018-02-21
  Type: Initial release
• Version 1.1: 2018-03-07
  Type: Database references