3B7E

Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural characterization of the 1918 influenza virus H1N1 neuraminidase

Xu, X.Zhu, X.Dwek, R.A.Stevens, J.Wilson, I.A.

(2008) J.Virol. 82: 10493-10501

  • DOI: 10.1128/JVI.00959-08
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 "Spanish flu" (A/Brevig M ...

    Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 "Spanish flu" (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-A and 1.45-A resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147 to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A, B
385Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for Q9IGQ6 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Go to UniProtKB:  Q9IGQ6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
ZMR
Query on ZMR

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Download CCD File 
A, B
ZANAMIVIR
MODIFIED SIALIC ACID
C12 H20 N4 O7
ARAIBEBZBOPLMB-UFGQHTETSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMRIC50: 0.5 - 5 nM (93) BINDINGDB
ZMRKi: 0.4 - 1 nM (90) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.044α = 90.00
b = 129.247β = 90.00
c = 118.845γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2011-10-12
    Type: Derived calculations
  • Version 1.3: 2017-10-25
    Type: Refinement description