Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 182.10 kDa 
• Atom Count: 13064 
• Residue Count: 1552 
• Unique protein chains: 1

4GZX

N2 neuraminidase D151G mutant of A/Tanzania/205/2010 H3N2 in complex with human sialic acid receptor

• DOI: 10.2210/pdb4GZX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): H3N2 subtype
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-09-06 Released: 2012-10-17 
• Deposition Author(s): Zhu, X., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.271 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors.

Zhu, X., McBride, R., Nycholat, C.M., Yu, W., Paulson, J.C., Wilson, I.A.

(2012) J Virol 86: 13371-13383

• PubMed: 23015718 
• DOI: 10.1128/JVI.01426-12
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Influenza virus neuraminidase (NA) cleaves off sialic acid from cellular receptors of hemagglutinin (HA) to enable progeny escape from infected cells. However, NA variants (D151G) of recent human H3N2 viruses have also been reported to bind receptors on red blood cells, but the nature of these receptors and the effect of the mutation on NA activity were not established. Here, we compare the functional and structural properties of a human H3N2 NA from A/Tanzania/205/2010 and its D151G mutant, which supports HA-independent receptor binding. While the wild-type NA efficiently cleaves sialic acid from both α2-6- and α2-3-linked glycans, the mutant exhibits much reduced enzymatic activity toward both types of sialosides. Conversely, while wild-type NA shows no detectable binding to sialosides, the D151G NA exhibits avid binding with broad specificity toward α2-3 sialosides. D151G NA binds the 3' sialyllactosamine (3'-SLN) and 6'-SLN sialosides with equilibrium dissociation constant (K(D)) values of 30.0 μM and 645 μM, respectively, which correspond to much higher affinities than the corresponding affinities (low mM) of HA to these glycans. Crystal structures of wild-type and mutant NAs reveal the structural basis for glycan binding in the active site by exclusively impairing the glycosidic bond hydrolysis step. The general significance of D151 among influenza virus NAs was further explored by introducing the D151G mutation into three N1 NAs and one N2 NA, which all exhibited reduced enzymatic activity and preferential binding to α2-3 sialosides. Since the enzymatic and binding activities of NAs are not routinely assessed, the potential for NA receptor binding to contribute to influenza virus biology may be underappreciated.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
neuraminidase	A, B, C, D	393	H3N2 subtype	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
Find proteins for K7N5N3 (H3N2 subtype) Go to UniProtKB:  K7N5N3

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	A, B, C, D	O-SIALIC ACID C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GAL	A, B	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
BMA	A, B, C, D	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	A, B, C, D	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	C	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
FUL	D	BETA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SIA	Kd :  645000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.271 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.587	α = 90
b = 110.176	β = 97.45
c = 110.043	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-06 
• Released Date: 2012-10-17 
Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History 

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references