4NRK

Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40 complex with LSTc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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This is version 2.0 of the entry. See complete history


Literature

The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus.

Ni, F.Nnadi Mbawuike, I.Kondrashkina, E.Wang, Q.

(2014) Virology 450-451: 71-83

  • DOI: https://doi.org/10.1016/j.virol.2013.11.038
  • Primary Citation of Related Structures:  
    4NRJ, 4NRK, 4NRL

  • PubMed Abstract: 

    Diverged ~4000 years ago, influenza B virus has several important differences from influenza A virus, including lower receptor-binding affinity and highly restricted host range. Based on our prior structural studies, we hypothesized that a single-residue difference in the receptor-binding site of hemagglutinin (HA), Phe-95 in influenza B virus versus Tyr-98 in influenza A/H1-H15, is possibly a key determinant for the low receptor-binding affinity. Here we demonstrate that the mutation Phe95→Tyr in influenza B virus HA restores all three hydrogen bonds made by Tyr-98 in influenza A/H1-15 HA and has the potential to enhance receptor binding. However, the full realization of this potential is influenced by the local environment into which the mutation is introduced. The binding and replication of the recombinant viruses correlate well with the receptor-binding capabilities of HA. These results are discussed in relation to the roles of Phe-95 in receptor binding and pathogenicity of influenza B virus.


  • 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, 6100 Main Street, Houston, TX 77005, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
346Influenza B virus (B/Lee/1940)Mutation(s): 1 
Gene Names: HA
UniProt
Find proteins for P03460 (Influenza B virus (strain B/Lee/1940))
Explore P03460 
Go to UniProtKB:  P03460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03460
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
182Influenza B virus (B/Lee/1940)Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03460 (Influenza B virus (strain B/Lee/1940))
Explore P03460 
Go to UniProtKB:  P03460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03460
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, L
G, H, I, J, L, N, O, Q, R, S, T, U
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, P, V
3N/A
Glycosylation Resources
GlyTouCan:  G73578JC
GlyCosmos:  G73578JC
GlyGen:  G73578JC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.61α = 90
b = 128.3β = 90
c = 211.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary