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 
  • R-Value Observed: 0.141 

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
  • Structures With Same Primary Citation

  • 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 virusMutation(s): 0 
Gene Names: Neuraminidase
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
ZMR
Query on ZMR

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

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUC
Query on FUC

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

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMRIC50:  5.900000095367432   nM  BindingDB
ZMRIC50:  0.5   nM  BindingDB
ZMRIC50:  1.2000000476837158   nM  BindingDB
ZMRIC50:  5.400000095367432   nM  BindingDB
ZMRIC50:  0.699999988079071   nM  BindingDB
ZMRIC50:  0.800000011920929   nM  BindingDB
ZMRIC50:  4.199999809265137   nM  BindingDB
ZMRIC50:  2.5   nM  BindingDB
ZMRIC50:  0.5799999833106995   nM  BindingDB
ZMRIC50:  45   nM  BindingDB
ZMRIC50:  5   nM  BindingDB
ZMRIC50:  1.7999999523162842   nM  BindingDB
ZMRKi:  0.4000000059604645   nM  BindingDB
ZMRIC50:  2.4000000953674316   nM  BindingDB
ZMRIC50:  1.559999942779541   nM  BindingDB
ZMRIC50:  12   nM  BindingDB
ZMRKi:  1   nM  BindingDB
ZMRIC50:  1.7000000476837158   nM  BindingDB
ZMRIC50:  2.9000000953674316   nM  BindingDB
ZMRIC50:  2.299999952316284   nM  BindingDB
ZMRIC50:  2   nM  BindingDB
ZMRIC50:  4.800000190734863   nM  BindingDB
ZMRIC50:  6   nM  BindingDB
ZMRKi:  0.5   nM  BindingDB
ZMRIC50:  0.800000011920929   nM  BindingDB
ZMRIC50:  1.100000023841858   nM  BindingDB
ZMRIC50:  1.899999976158142   nM  BindingDB
ZMRIC50:  3.5   nM  BindingDB
ZMRIC50:  9.100000381469727   nM  BindingDB
ZMRIC50:  0.6000000238418579   nM  BindingDB
ZMRIC50:  1.7999999523162842   nM  BindingDB
ZMRIC50:  1.399999976158142   nM  BindingDB
ZMRIC50:  2.200000047683716   nM  BindingDB
ZMRIC50:  0.4699999988079071   nM  BindingDB
ZMRIC50:  0.699999988079071   nM  BindingDB
ZMRIC50:  2.299999952316284   nM  BindingDB
ZMRIC50:  5.5   nM  BindingDB
ZMRIC50:  12   nM  BindingDB
ZMRIC50:  4   nM  BindingDB
ZMRIC50:  1.600000023841858   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.044α = 90
b = 129.247β = 90
c = 118.845γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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