5YR9 | pdb_00005yr9

Crystal Structure of Cypovirus Polyhedra R13A/E73C/Y83C Mutant

• PDB DOI: https://doi.org/10.2210/pdb5YR9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bombyx mori cypovirus 1
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-11-08 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: 1.70 Å
• R-Value Free: 
  0.205 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

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: https://doi.org/10.1039/c7cc08689j
• Primary Citation Related Structures: 
  5YR1, 5YR9, 5YRA, 5YRB, 5YRC, 5YRD


• 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].

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (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: 28.57 kDa 
• Atom Count: 2,066 
• Modeled Residue Count: 236 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.205 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.75	α = 90
b = 103.75	β = 90
c = 103.75	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary