7U4F | pdb_00007u4f

Neuraminidase from influenza virus A/Moscow/10/1999(H3N2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.165 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase.

Lei, R.Tan, T.J.C.Hernandez Garcia, A.Wang, Y.Diefenbacher, M.Teo, C.Gopan, G.Tavakoli Dargani, Z.Teo, Q.W.Graham, C.S.Brooke, C.B.Nair, S.K.Wu, N.C.

(2022) Nat Commun 13: 6443-6443

  • DOI: https://doi.org/10.1038/s41467-022-34060-8
  • Primary Citation Related Structures: 
    7U4E, 7U4F, 7U4G

  • PubMed Abstract: 

    Neuraminidase (NA) of human influenza H3N2 virus has evolved rapidly and been accumulating mutations for more than half-century. However, biophysical constraints that govern the evolutionary trajectories of NA remain largely elusive. Here, we show that among 70 natural mutations that are present in the NA of a recent human H3N2 strain, >10% are deleterious for an ancestral strain. By mapping the permissive mutations using combinatorial mutagenesis and next-generation sequencing, an extensive epistatic network is revealed. Biophysical and structural analyses further demonstrate that certain epistatic interactions can be explained by non-additive stability effect, which in turn modulates membrane trafficking and enzymatic activity of NA. Additionally, our results suggest that other biophysical mechanisms also contribute to epistasis in NA evolution. Overall, these findings not only provide mechanistic insights into the evolution of human influenza NA and elucidate its sequence-structure-function relationship, but also have important implications for the development of next-generation influenza vaccines.


  • Organizational Affiliation
    • Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Macromolecule Content 

  • Total Structure Weight: 45.2 kDa 
  • Atom Count: 3,760 
  • Modeled Residue Count: 388 
  • Deposited Residue Count: 393 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuraminidase393Influenza A virus (A/Moscow/10/1999(H3N2))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for Q8AZ87 (Influenza A virus)
Explore Q8AZ87 
Go to UniProtKB:  Q8AZ87
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8AZ87
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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
B
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G90333CG
GlyCosmos: G90333CG
GlyGen: G90333CG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.165 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.153α = 90
b = 136.153β = 90
c = 150.767γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR00 AI139445
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesDP2 AT011966
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI167910

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary