9EQN

N-terminal domain of Infectious Bursal Disease Virus (IBDV) VP3

• PDB DOI: https://doi.org/10.2210/pdb9EQN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Infectious bursal disease virus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-03-22 Released: 2024-10-09 
• Deposition Author(s): Ferrero, D.S., Verdaguer, N.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Structure of the amino terminal domain of the Birnaviral multifunctional VP3 protein and its unexplored critical role

Ferrero, D.S., Verdaguer, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.28 kDa 
• Atom Count: 2,408 
• Modelled Residue Count: 276 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural polyprotein	A, B, C, D	75	Infectious bursal disease virus	Mutation(s): 0
UniProt
Find proteins for P61825 (Avian infectious bursal disease virus) Explore P61825  Go to UniProtKB:  P61825

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EOH	E [auth C]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.67	α = 90
b = 55.761	β = 110.1
c = 52.894	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
Arcimboldo	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Ferrero, D.S., Verdaguer, N.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-117976GB-I00

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release