Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 181.72 kDa 
• Atom Count: 13064 
• Modelled Residue Count: 1552 
• Deposited Residue Count: 1572 
• Unique protein chains: 1

4GZX

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

• PDB 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
• Primary Citation of Related Structures:  
  4GZO, 4GZP, 4GZQ, 4GZS, 4GZT, 4GZW, 4GZX


• 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	Image
neuraminidase	A, B, C, D	393	H3N2 subtype	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for K7N5N3 (H3N2 subtype) Explore K7N5N3  Go to UniProtKB:  K7N5N3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	E, G	2		N/A
Glycosylation Resources
GlyTouCan:  G63069TR GlyCosmos:  G63069TR GlyGen:  G63069TR

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, I, K	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G95595RA GlyCosmos:  G95595RA GlyGen:  G95595RA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	V [auth C], Z [auth D]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	AA [auth D], BA [auth D], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	CA [auth D], P [auth A], Q [auth A], U [auth B], Y [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SIA	PDBBind:  4GZX	Kd: 6.45e+5 (nM) from 1 assay(s)

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
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary