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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 177.18 kDa 
• Atom Count: 11163 
• Modelled Residue Count: 1374 
• Deposited Residue Count: 1533 
• Unique protein chains: 2

6E7H

Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus in complex with 3'-GcLN

• PDB DOI: 10.2210/pdb6E7H/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1))
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2018-07-26 Released: 2019-06-19 
• Deposition Author(s): Tzarum, N., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.280 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 

Literature

N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses.

Broszeit, F., Tzarum, N., Zhu, X., Nemanichvili, N., Eggink, D., Leenders, T., Li, Z., Liu, L., Wolfert, M.A., Papanikolaou, A., Martinez-Romero, C., Gagarinov, I.A., Yu, W., Garcia-Sastre, A., Wennekes, T., Okamatsu, M., Verheije, M.H., Wilson, I.A., Boons, G.J., de Vries, R.P.

(2019) Cell Rep 27: 3284-3294.e6

• PubMed: 31189111 
• DOI: 10.1016/j.celrep.2019.05.048
• Primary Citation of Related Structures:  
  6E7G, 6E7H, 6N5A


• PubMed Abstract: 
  

A species barrier for the influenza A virus is the differential expression of sialic acid, which can either be α2,3-linked for avians or α2,6-linked for human viruses. The influenza A virus hosts also express other species-specific sialic acid derivatives. One major modification at C-5 is N-glycolyl (NeuGc), instead of N-acetyl (NeuAc). N-glycolyl is mammalian specific and expressed in pigs and horses, but not in humans, ferrets, seals, or dogs. Hemagglutinin (HA) adaptation to either N-acetyl or N-glycolyl is analyzed on a sialoside microarray containing both α2,3- and α2,6-linkage modifications on biologically relevant N-glycans. Binding studies reveal that avian, human, and equine HAs bind either N-glycolyl or N-acetyl. Structural data on N-glycolyl binding HA proteins of both H5 and H7 origin describe this specificity. Neuraminidases can cleave N-glycolyl efficiently, and tissue-binding studies reveal strict species specificity. The exclusive manner in which influenza A viruses differentiate between N-glycolyl and N-acetyl is indicative of selection.

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Organizational Affiliation: 

Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, the Netherlands. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 1  Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus) Explore Q6DQ33  Go to UniProtKB:  Q6DQ33

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	177	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q6DQ18 (Influenza A virus (strain A/Chicken/Hong Kong/YU22/2002 H5N1 genotype Z)) Explore Q6DQ18  Go to UniProtKB:  Q6DQ18

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, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	I	2		N/A
Glycosylation Resources
GlyTouCan:  G38557KR GlyCosmos:  G38557KR GlyGen:  G38557KR

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.280 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.555	α = 90
b = 231.07	β = 97.04
c = 71.295	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-26 
• Released Date: 2019-06-19 
Deposition Author(s): Tzarum, N., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-06-26
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary