3RO5 | pdb_00003ro5

Crystal structure of influenza A virus nucleoprotein with ligand

• PDB DOI: https://doi.org/10.2210/pdb3RO5/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Wilson-Smith/1933(H1N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-25 Released: 2011-09-14 
• Deposition Author(s): Pearce, B.C., Edavettal, S., McDonnell, P.A., Lewis, H.A., Steinbacher, S., Baldwin, E.T., Langley, D.R., Maskos, K., Mortl, M., Kiefersauer, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.280 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Literature

Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers.

Gerritz, S.W., Cianci, C., Kim, S., Pearce, B.C., Deminie, C., Discotto, L., McAuliffe, B., Minassian, B.F., Shi, S., Zhu, S., Zhai, W., Pendri, A., Li, G., Poss, M.A., Edavettal, S., McDonnell, P.A., Lewis, H.A., Maskos, K., Mortl, M., Kiefersauer, R., Steinbacher, S., Baldwin, E.T., Metzler, W., Bryson, J., Healy, M.D., Philip, T., Zoeckler, M., Schartman, R., Sinz, M., Leyva-Grado, V.H., Hoffmann, H.H., Langley, D.R., Meanwell, N.A., Krystal, M.

(2011) Proc Natl Acad Sci U S A 108: 15366-15371

• PubMed: 21896751 
• DOI: https://doi.org/10.1073/pnas.1107906108
• Primary Citation Related Structures: 
  3RO5


• PubMed Abstract: 
  

  Influenza nucleoprotein (NP) plays multiple roles in the virus life cycle, including an essential function in viral replication as an integral component of the ribonucleoprotein complex, associating with viral RNA and polymerase within the viral core. The multifunctional nature of NP makes it an attractive target for antiviral intervention, and inhibitors targeting this protein have recently been reported. In a parallel effort, we discovered a structurally similar series of influenza replication inhibitors and show that they interfere with NP-dependent processes via formation of higher-order NP oligomers. Support for this unique mechanism is provided by site-directed mutagenesis studies, biophysical characterization of the oligomeric ligand:NP complex, and an X-ray cocrystal structure of an NP dimer of trimers (or hexamer) comprising three NP_A:NP_B dimeric subunits. Each NP_A:NP_B dimeric subunit contains two ligands that bridge two composite, protein-spanning binding sites in an antiparallel orientation to form a stable quaternary complex. Optimization of the initial screening hit produced an analog that protects mice from influenza-induced weight loss and mortality by reducing viral titers to undetectable levels throughout the course of treatment.

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Organizational Affiliation: 
• Bristol-Myers Squibb Research and Development, Wallingford, CT 06492, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 114.53 kDa 
• Atom Count: 6,341 
• Modeled Residue Count: 853 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein	A, B	499	Influenza A virus (A/Wilson-Smith/1933(H1N1))	Mutation(s): 0  Gene Names: NP
UniProt
Find proteins for Q1K9H2 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1)) Explore Q1K9H2  Go to UniProtKB:  Q1K9H2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGH	C [auth B], D [auth B]	[4-(2-chloro-4-nitrophenyl)piperazin-1-yl][3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]methanone C22 H21 Cl N4 O5 OQYUKAFYGKRXTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.280 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.2	α = 90
b = 146.2	β = 90
c = 146.2	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-14 
Deposition Author(s): Pearce, B.C., Edavettal, S., McDonnell, P.A., Lewis, H.A., Steinbacher, S., Baldwin, E.T., Langley, D.R., Maskos, K., Mortl, M., Kiefersauer, R.

Revision History  

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Database references
• Version 1.2: 2011-09-28
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations