Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 169.66 kDa 
• Atom Count: 11820 
• Modelled Residue Count: 1465 
• Deposited Residue Count: 1509 
• Unique protein chains: 2

4XQ5

Human-infecting H10N8 influenza virus retains strong preference for avian-type receptors

• PDB DOI: 10.2210/pdb4XQ5/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Jiangxi/IPB13/2013(H10N8))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-01-19 Released: 2015-04-01 
• Deposition Author(s): Tzarum, N., Zhang, H., Zhu, X., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.230 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

A Human-Infecting H10N8 Influenza Virus Retains a Strong Preference for Avian-type Receptors.

Zhang, H., de Vries, R.P., Tzarum, N., Zhu, X., Yu, W., McBride, R., Paulson, J.C., Wilson, I.A.

(2015) Cell Host Microbe 17: 377-384

• PubMed: 25766296 
• DOI: 10.1016/j.chom.2015.02.006
• Primary Citation of Related Structures:  
  4XQ5, 4XQO, 4XQU


• PubMed Abstract: 
  

Recent avian-origin H10N8 influenza A viruses that have infected humans pose a potential pandemic threat. Alterations in the viral surface glycoprotein, hemagglutinin (HA), typically are required for influenza A viruses to cross the species barrier for adaptation to a new host, but whether H10N8 contains adaptations supporting human infection remains incompletely understood. We investigated whether H10N8 HA can bind human receptors. Sialoside glycan microarray analysis showed that the H10 HA retains a strong preference for avian receptor analogs and negligible binding to human receptor analogs. Crystal structures of H10 HA with avian and human receptor analogs revealed the basis for preferential recognition of avian-like receptors. Furthermore, introduction of mutations into the H10 receptor-binding site (RBS) known to convert other HA subtypes from avian to human receptor specificity failed to switch preference to human receptors. Collectively, these findings suggest that the current H10N8 human isolates are poorly adapted for efficient human-to-human transmission.

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Organizational Affiliation: 

Department of Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	323	Influenza A virus (A/Jiangxi/IPB13/2013(H10N8))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1  Go to UniProtKB:  A0A059T4A1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	180	Influenza A virus (A/Jiangxi/IPB13/2013(H10N8))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1  Go to UniProtKB:  A0A059T4A1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.230 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.069	α = 90
b = 242.992	β = 111.26
c = 70.381	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing
PHENIX	model building
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-19 
• Released Date: 2015-04-01 
Deposition Author(s): Tzarum, N., Zhang, H., Zhu, X., Wilson, I.A.

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-09-01
  Changes: Database references, Derived calculations, Structure summary