7U4E

Neuraminidase from influenza virus A/Bilthoven/17938/1969(H3N2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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This is version 1.2 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D
469Influenza A virus (A/Bilthoven/17938/1969(H3N2))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for H9XI12 (Influenza A virus)
Explore H9XI12 
Go to UniProtKB:  H9XI12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9XI12
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-glucopyranoseE [auth F],
F [auth G],
G [auth H],
H [auth K]
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G01760ZU
GlyCosmos:  G01760ZU
GlyGen:  G01760ZU
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
O [auth C],
R [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
P [auth C],
S [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth A],
N [auth B],
Q [auth C],
T [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.339α = 90
b = 137.944β = 92.15
c = 138.246γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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