6TZB | pdb_00006tzb

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in complex with 6'-SLNLN

• PDB DOI: https://doi.org/10.2210/pdb6TZB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-08-12 Released: 2019-10-30 
• Deposition Author(s): Wu, N.C., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.207 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.157 (Depositor) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape.

Wu, N.C., Otwinowski, J., Thompson, A.J., Nycholat, C.M., Nourmohammad, A., Wilson, I.A.

(2020) Nat Commun 11: 1233-1233

• PubMed: 32144244 
• DOI: https://doi.org/10.1038/s41467-020-15102-5
• Primary Citation Related Structures: 
  6TZB


• PubMed Abstract: 
  

  Antigenic drift of influenza virus hemagglutinin (HA) is enabled by facile evolvability. However, HA antigenic site B, which has become immunodominant in recent human H3N2 influenza viruses, is also evolutionarily constrained by its involvement in receptor binding. Here, we employ deep mutational scanning to probe the local fitness landscape of HA antigenic site B in six different human H3N2 strains spanning from 1968 to 2016. We observe that the fitness landscape of HA antigenic site B can be very different between strains. Sequence variants that exhibit high fitness in one strain can be deleterious in another, indicating that the evolutionary constraints of antigenic site B have changed over time. Structural analysis suggests that the local fitness landscape of antigenic site B can be reshaped by natural mutations via modulation of the receptor-binding mode. Overall, these findings elucidate how influenza virus continues to explore new antigenic space despite strong functional constraints.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Max Planck Institute for Dynamics and Self-Organization, 37077, Göttingen, Germany.
Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Department of Physics, University of Washington, Seattle, WA, 98195, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].
The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 174.94 kDa 
• Atom Count: 12,998 
• Modeled Residue Count: 1,469 
• Deposited Residue Count: 1,491 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	321	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7  Go to UniProtKB:  Q91MA7
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	176	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for H9XC94 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore H9XC94  Go to UniProtKB:  H9XC94
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

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

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

Entity ID: 5
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-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, Q	5		N/A
Glycosylation Resources
GlyTouCan: G60430KO GlyCosmos: G60430KO GlyGen: G60430KO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	K	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 7
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	M	3		N/A
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	R [auth A], S [auth C], T [auth C], U [auth D], V [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046	M	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.207 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.157 (Depositor) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.401	α = 90
b = 132.173	β = 97.93
c = 72.468	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Wu, N.C., 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 AI127371
Bill & Melinda Gates Foundation	United States	OPP1170236

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2020-03-25
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary