9BJL

Crystal structure of Influenza D virus Nucleoprotein (Oklahoma)

• PDB DOI: https://doi.org/10.2210/pdb9BJL/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza D virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-25 Released: 2024-05-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.241 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Crystal structure of Influenza D virus Nucleoprotein (Oklahoma)

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (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: 253.67 kDa 
• Atom Count: 14,456 
• Modelled Residue Count: 1,837 
• Deposited Residue Count: 2,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	571	Influenza D virus	Mutation(s): 0  Gene Names: NP
UniProt
Find proteins for W5RBB9 (Influenza D virus) Explore W5RBB9  Go to UniProtKB:  W5RBB9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.241 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m39bjl

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.461	α = 102.34
b = 84.501	β = 97.37
c = 88.728	γ = 97.14

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release