4KDO | pdb_00004kdo

Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with human receptor analog LSTc

• PDB DOI: https://doi.org/10.2210/pdb4KDO/pdb

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


• Deposited: 2013-04-25 Released: 2013-07-24 
• Deposition Author(s): Lu, X., Shi, Y., Zhang, W., Zhang, Y., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut).

Lu, X., Shi, Y., Zhang, W., Zhang, Y., Qi, J., Gao, G.F.

(2013) Protein Cell 4: 502-511

• PubMed: 23794001 
• DOI: https://doi.org/10.1007/s13238-013-3906-z
• Primary Citation Related Structures: 
  4KDM, 4KDN, 4KDO, 4KDQ


• PubMed Abstract: 
  

  Avian influenza A virus continues to pose a global threat with occasional H5N1 human infections, which is emphasized by a recent severe human infection caused by avian-origin H7N9 in China. Luckily these viruses do not transmit efficiently in human populations. With a few amino acid substitutions of the hemagglutinin H5 protein in the laboratory, two H5 mutants have been shown to obtain an air-borne transmission in a mammalian ferret model. Here in this study one of the mutant H5 proteins developed by Kawaoka's group (VN1203mut) was expressed in a baculovirus system and its receptor-binding properties were assessed. We herein show that the VN1203mut had a dramatically reduced binding affinity for the avian α2,3-linkage receptor compared to wild type but showed no detectable increase in affinity for the human α2,6-linkage receptor, using Surface Plasmon Resonance techonology. Further, the crystal structures of the VN1203mut and its complexes with either human or avian receptors demonstrate that the VN1203mut binds the human receptor in the same binding manner (cis conformation) as seen for the HAs of previously reported 1957 and 1968 pandemic influenza viruses. Our receptor binding and crystallographic data shown here further confirm that the ability to bind the avian receptor has to decrease for a higher human receptor binding affinity. As the Q226L substitution is shown important for obtaining human receptor binding, we suspect that the newly emerged H7N9 binds human receptor as H7 has a Q226L substitution.

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Organizational Affiliation: 
• College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 172.33 kDa 
• Atom Count: 12,373 
• Modeled Residue Count: 1,491 
• Deposited Residue Count: 1,491 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth C], C [auth E]	322	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 4  Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33  Go to UniProtKB:  Q6DQ33
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	D [auth B], E [auth D], F	175	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33  Go to UniProtKB:  Q6DQ33

Oligosaccharides

Help  

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N/A
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	K [auth A]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046	I	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.257	α = 90
b = 245.913	β = 112.96
c = 69.569	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Lu, X., Shi, Y., Zhang, W., Zhang, Y., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2014-10-29
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary