5YRA

Crystal Structure of Cypovirus Polyhedra R13A/S193C/A194C Mutant

PDB DOI: https://doi.org/10.2210/pdb5YRA/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.218
R-Value Work: 0.158
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1039/c7cc08689j
Primary Citation of 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.

Organizational Affiliation

School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. saabe@bio.titech.ac.jp tueno@bio.titech.ac.jp.

Macromolecule Content

Total Structure Weight: 28.89 kDa
Atom Count: 2,105
Modelled Residue Count: 241
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11041
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]