4O46

14-3-3-gamma in complex with influenza NS1 C-terminal tail phosphorylated at S228

• PDB DOI:  https://doi.org/10.2210/pdb4O46/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Influenza A virus H3N2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-18 Released: 2014-04-30 
• Deposition Author(s): Qin, S., Liu, Y., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.

Qin, S., Liu, Y., Tempel, W., Eram, M.S., Bian, C., Liu, K., Senisterra, G., Crombet, L., Vedadi, M., Min, J.

(2014) Nat Commun 5: 3952-3952

• PubMed: 24853335 
• DOI: https://doi.org/10.1038/ncomms4952
• Primary Citation of Related Structures:  
  4NW2, 4O42, 4O45, 4O46


• PubMed Abstract: 
  

Pathogens can interfere with vital biological processes of their host by mimicking host proteins. The NS1 protein of the influenza A H3N2 subtype possesses a histone H3K4-like sequence at its carboxyl terminus and has been reported to use this mimic to hijack host proteins. However, this mimic lacks a free N-terminus that is essential for binding to many known H3K4 readers. Here we show that the double chromodomains of CHD1 adopt an 'open pocket' to interact with the free N-terminal amine of H3K4, and the open pocket permits the NS1 mimic to bind in a distinct conformation. We also explored the possibility that NS1 hijacks other cellular proteins and found that the NS1 mimic has access to only a subset of chromatin-associated factors, such as WDR5. Moreover, methylation of the NS1 mimic can not be reversed by the H3K4 demethylase LSD1. Overall, we thus conclude that the NS1 mimic is an imperfect histone mimic.

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Organizational Affiliation: 

1] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China [2] Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada M5G 1L7 [3] Department of Physiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 196.44 kDa 
• Atom Count: 10,919 
• Modelled Residue Count: 1,465 
• Deposited Residue Count: 1,722 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein gamma	A, B, C, D, E, F	256	Homo sapiens	Mutation(s): 0  Gene Names: YWHAG
UniProt & NIH Common Fund Data Resources
Find proteins for P61981 (Homo sapiens) Explore P61981  Go to UniProtKB:  P61981
PHAROS:  P61981

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonstructural protein 1	G, H, I, J, K, L	15	Influenza A virus H3N2	Mutation(s): 0  Gene Names: NS
UniProt
Find proteins for Q9YP60 (Influenza A virus H3N2) Explore Q9YP60  Go to UniProtKB:  Q9YP60

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified polymer	M, N, O, P [auth V]	24	Homo sapiens	Mutation(s): 0  Gene Names: YWHAG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IA [auth B], IB [auth D], JA [auth B], JB [auth D], KA [auth B], KB [auth D], LA [auth B], LB [auth D], MA [auth B], MB [auth D], NA [auth B], NB [auth D], OA [auth B], OB [auth D], PA [auth B], PB [auth E], Q [auth A], QA [auth B], QB [auth E], R [auth A], RA [auth B], RB [auth E], S [auth A], SA [auth C], SB [auth E], T [auth A], TA [auth C], TB [auth E], U [auth A], UA [auth C], UB [auth F], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	G, H, I, J, K, L	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.829	α = 90
b = 121.829	β = 90
c = 314.221	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Qin, S., Liu, Y., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2014-06-04
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description