1USX

Crystal structure of the Newcastle disease virus hemagglutinin-neuraminidase complexed with thiosialoside

• PDB DOI: https://doi.org/10.2210/pdb1USX/pdb

• Classification: HYDROLASE
• Organism(s): avian paramyxovirus 1
• Mutation(s): No 


• Deposited: 2003-12-01 Released: 2004-03-19 
• Deposition Author(s): Zaitsev, V., Itzstein, M., Groves, D., Kiefel, M., Takimoto, T., Portner, A., Taylor, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.289 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Second Sialic Acid Binding Site in Newcastle Disease Virus Hemagglutinin-Neuraminidase: Implications for Fusion

Zaitsev, V., Von Itzstein, M., Groves, D., Kiefel, M., Takimoto, T., Portner, A., Taylor, G.

(2004) J Virol 78: 3733

• PubMed: 15016893 
• DOI: https://doi.org/10.1128/jvi.78.7.3733-3741.2004
• Primary Citation of Related Structures:  
  1USR, 1USX


• PubMed Abstract: 
  

  Paramyxoviruses are the leading cause of respiratory disease in children. Several paramyxoviruses possess a surface glycoprotein, the hemagglutinin-neuraminidase (HN), that is involved in attachment to sialic acid receptors, promotion of fusion, and removal of sialic acid from infected cells and progeny virions. Previously we showed that Newcastle disease virus (NDV) HN contained a pliable sialic acid recognition site that could take two states, a binding state and a catalytic state. Here we present evidence for a second sialic acid binding site at the dimer interface of HN and present a model for its involvement in cell fusion. Three different crystal forms of NDV HN now reveal identical tetrameric arrangements of HN monomers, perhaps indicative of the tetramer association found on the viral surface.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 151.95 kDa 
• Atom Count: 10,497 
• Modelled Residue Count: 1,341 
• Deposited Residue Count: 1,362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN	A, B, C	454	avian paramyxovirus 1	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for P32884 (Newcastle disease virus (strain Beaudette C/45)) Explore P32884  Go to UniProtKB:  P32884

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-methyl 6-thio-beta-D-galactopyranoside	D, E, F	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G18879GM GlyCosmos:  G18879GM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAN	G [auth A], H [auth B], I [auth C]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C11 H17 N O8 JINJZWSZQKHCIP-UFGQHTETSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.289 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.07	α = 90
b = 115.07	β = 90
c = 283.96	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-19 
Deposition Author(s): Zaitsev, V., Itzstein, M., Groves, D., Kiefel, M., Takimoto, T., Portner, A., Taylor, G.

Revision History  

• Version 1.0: 2004-03-19
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Derived calculations, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2020-03-04
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-01
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary