6I3H | pdb_00006i3h

Crystal structure of influenza A virus M1 N-terminal domain (G18A mutation)

• PDB DOI: https://doi.org/10.2210/pdb6I3H/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-11-06 Released: 2019-09-18 
• Deposition Author(s): Miyake, Y., Keusch, J.J., Decamps, L., Ho-Xuan, H., Iketani, S., Gut, H., Kutay, U., Helenius, A., Yamauchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Influenza virus uses transportin 1 for vRNP debundling during cell entry.

Miyake, Y., Keusch, J.J., Decamps, L., Ho-Xuan, H., Iketani, S., Gut, H., Kutay, U., Helenius, A., Yamauchi, Y.

(2019) Nat Microbiol 4: 578-586

• PubMed: 30692667 
• DOI: https://doi.org/10.1038/s41564-018-0332-2
• Primary Citation Related Structures: 
  6I3H


• PubMed Abstract: 
  

  Influenza A virus is a pathogen of great medical impact. To develop novel antiviral strategies, it is essential to understand the molecular aspects of virus-host cell interactions in detail. During entry, the viral ribonucleoproteins (vRNPs) that carry the RNA genome must be released from the incoming particle before they can enter the nucleus for replication. The uncoating process is facilitated by histone deacetylase 6 (ref. ¹ ). However, the precise mechanism of shell opening and vRNP debundling is unknown. Here, we show that transportin 1, a member of the importin-β family proteins, binds to a PY-NLS ² sequence motif close to the amino terminus of matrix protein (M1) exposed during acid priming of the viral core. It promotes the removal of M1 and induces disassembly of vRNP bundles. Next, the vRNPs interact with importin-α/β and enter the nucleus. Thus, influenza A virus uses dual importin-βs for distinct steps in host cell entry.

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Organizational Affiliation: 
• School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK.
Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.26 kDa 
• Atom Count: 2,675 
• Modeled Residue Count: 322 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein 1	A, B	177	Influenza A virus	Mutation(s): 1
UniProt
Find proteins for P05777 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1)) Explore P05777  Go to UniProtKB:  P05777

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.56	α = 89.71
b = 35.58	β = 84.4
c = 69.29	γ = 69.02

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Miyake, Y., Keusch, J.J., Decamps, L., Ho-Xuan, H., Iketani, S., Gut, H., Kutay, U., Helenius, A., Yamauchi, Y.

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Funding Organization	Location	Grant Number
	Switzerland	--

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description