2GX9

X-ray structure of influenza virus NS1 effector domain

• PDB DOI: https://doi.org/10.2210/pdb2GX9/pdb

• Classification: TRANSCRIPTION, VIRUS/VIRAL PROTEIN
• Organism(s): unidentified influenza virus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-08 Released: 2006-05-30 
• Deposition Author(s): Bornholdt, Z.A., Prasad, B.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.223 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

X-ray structure of influenza virus NS1 effector domain.

Bornholdt, Z.A., Prasad, B.V.

(2006) Nat Struct Mol Biol 13: 559-560

• PubMed: 16715094 
• DOI: https://doi.org/10.1038/nsmb1099
• Primary Citation of Related Structures:  
  2GX9


• PubMed Abstract: 
  

  The nonstructural protein NS1 of influenza virus is an antagonist of host immune responses and is implicated in virulence. It has two domains, an N-terminal double-stranded RNA-binding domain (RBD) and an effector domain crucial for RBD function, for nuclear export and for sequestering messenger RNA-processing proteins. Here we present the crystallographic structure of the effector domain, which has a novel fold and suggests mechanisms for increased virulence in H5N1 strains.

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Organizational Affiliation: 

Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.65 kDa 
• Atom Count: 2,229 
• Modelled Residue Count: 249 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS1 Effector Domain	A, B	129	unidentified influenza virus	Mutation(s): 7  Gene Names: Segment 8 - NS1
UniProt
Find proteins for Q6LD08 (Influenza A virus) Explore Q6LD08  Go to UniProtKB:  Q6LD08

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN	C [auth A], D [auth A], E [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.223 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59	α = 90
b = 59	β = 90
c = 268.022	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-30 
Deposition Author(s): Bornholdt, Z.A., Prasad, B.V.

Revision History  

• Version 1.0: 2006-05-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2020-09-09
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary