5TJW

Influenza A virus Nucleoprotein in Complex with Inhibitory Nanobody

• PDB DOI: https://doi.org/10.2210/pdb5TJW/pdb

• Classification: Viral Protein/Immune System
• Organism(s): Influenza A virus (A/WSN/1933(H1N1)), Vicugna pacos
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-05 Released: 2016-12-21 
• Deposition Author(s): Hanke, L., Knockenhauer, K.E., Ploegh, H.L., Schwartz, T.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 0.262 
• R-Value Work: 0.204 
• R-Value Observed: 0.210 

Literature

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment.

Hanke, L., Knockenhauer, K.E., Brewer, R.C., van Diest, E., Schmidt, F.I., Schwartz, T.U., Ploegh, H.L.

(2016) mBio 7

• PubMed: 27965447 
• DOI: https://doi.org/10.1128/mBio.01569-16
• Primary Citation of Related Structures:  
  5TJW


• PubMed Abstract: 
  

  Alpaca-derived single-domain antibody fragments (VHHs) that target the influenza A virus nucleoprotein (NP) can protect cells from infection when expressed in the cytosol. We found that one such VHH, αNP-VHH1, exhibits antiviral activity similar to that of Mx proteins by blocking nuclear import of incoming viral ribonucleoproteins (vRNPs) and viral transcription and replication in the nucleus. We determined a 3.2-Å crystal structure of αNP-VHH1 in complex with influenza A virus NP. The VHH binds to a nonconserved region on the body domain of NP, which has been associated with binding to host factors and serves as a determinant of host range. Several of the NP/VHH interface residues determine sensitivity of NP to antiviral Mx GTPases. The structure of the NP/αNP-VHH1 complex affords a plausible explanation for the inhibitory properties of the VHH and suggests a rationale for the antiviral properties of Mx proteins. Such knowledge can be leveraged for much-needed novel antiviral strategies.

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Organizational Affiliation: 

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 72.52 kDa 
• Atom Count: 4,606 
• Modelled Residue Count: 589 
• Deposited Residue Count: 644 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	507	Influenza A virus (A/WSN/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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NP-specific inhibitory VHH	B [auth K]	137	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 0.262 
• R-Value Work: 0.204 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 3
• Diffraction Data: https://doi.org/10.15785/SBGRID/450

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.548	α = 90
b = 137.548	β = 90
c = 137.548	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Hanke, L., Knockenhauer, K.E., Ploegh, H.L., Schwartz, T.U.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-01-04
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description