Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 177.73 kDa 
• Atom Count: 12115 
• Residue Count: 1541 
• Unique protein chains: 2

4M40

Crystal structure of hemagglutinin of influenza virus B/Yamanashi/166/1998

• DOI: 10.2210/pdb4M40/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza B virus (B/Yamanashi/166/1998)
• Expression System: Mammalia
• Mutation(s): No 


• Deposited: 2013-08-06 Released: 2013-09-25 
• Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.54 Å
• R-Value Free: 0.244 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Structural basis for the divergent evolution of influenza B virus hemagglutinin.

Ni, F., Kondrashkina, E., Wang, Q.

(2013) Virology 446: 112-122

• PubMed: 24074573 
• DOI: 10.1016/j.virol.2013.07.035
• Primary Citation of Related Structures:  
  4M44, 4M40


• PubMed Abstract: 
  

Influenza A and B viruses are responsible for the severe morbidity and mortality worldwide in annual influenza epidemics. Currently circulating influenza B virus belongs to the B/Victoria or B/Yamagata lineage that was diverged from each other about 30-40 years ago. However, a mechanistic understanding of their divergent evolution is still lacking. Here we report the crystal structures of influenza B/Yamanashi/166/1998 hemagglutinin (HA) belonging to B/Yamagata lineage and its complex with the avian-like receptor analogue. Comparison of these structures with those of undiverged and diverged influenza B virus HAs, in conjunction with sequence analysis, reveals the molecular basis for the divergent evolution of influenza B virus HAs. Furthermore, HAs of diverged influenza B virus strains display much stronger molecular interactions with terminal sialic acid of bound receptors, which may allow for a different tissue tropism for current influenza B viruses, for which further investigation is required.

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Organizational Affiliation: 

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	346	Influenza B virus (B/Yamanashi/166/1998)	Mutation(s): 0  Gene Names: HA
Find proteins for A3DQM7 (Influenza B virus) Explore A3DQM7  Go to UniProtKB:  A3DQM7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	182	Influenza B virus (B/Yamanashi/166/1998)	Mutation(s): 0  Gene Names: HA
Find proteins for A3DQM7 (Influenza B virus) Explore A3DQM7  Go to UniProtKB:  A3DQM7

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, J, K, L, M, N, O	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, D, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.54 Å
• R-Value Free: 0.244 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.912	α = 90
b = 101.294	β = 115.18
c = 136.81	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASES	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-06 
• Released Date: 2013-09-25 
Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.

Revision History 

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary