Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.77 kDa 
• Atom Count: 7042 
• Modelled Residue Count: 770 
• Deposited Residue Count: 770 
• Unique protein chains: 1

3B7E

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

• DOI: 10.2210/pdb3B7E/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2007-10-30 Released: 2008-10-07 
• Deposition Author(s): Xu, X., Zhu, X., Wilson, I.A.

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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 

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

• PubMed: 18715929 
• DOI: 10.1128/JVI.00959-08
• Primary Citation of Related Structures:  
  3B7E, 3BEQ


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B	385	Influenza A virus	Mutation(s): 0  Gene Names: Neuraminidase EC: 3.2.1.18
UniProt
Find proteins for Q9IGQ6 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9IGQ6  Go to UniProtKB:  Q9IGQ6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80587NA GlyCosmos:  G80587NA GlyGen:  G80587NA

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZMR	H [auth A], O [auth B]	ZANAMIVIR C12 H20 N4 O7 ARAIBEBZBOPLMB-UFGQHTETSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth A],  J [auth A],  K [auth A],  L [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZMR	IC50:  5.900000095367432   nM  BindingDB
ZMR	IC50:  0.5   nM  BindingDB
ZMR	IC50:  5.300000190734863   nM  BindingDB
ZMR	IC50:  5.400000095367432   nM  BindingDB
ZMR	IC50:  0.699999988079071   nM  BindingDB
ZMR	IC50:  0.5799999833106995   nM  BindingDB
ZMR	IC50:  3.700000047683716   nM  BindingDB
ZMR	IC50:  8.100000381469727   nM  BindingDB
ZMR	IC50:  9.300000190734863   nM  BindingDB
ZMR	IC50:  9.800000190734863   nM  BindingDB
ZMR	IC50:  8.300000190734863   nM  BindingDB
ZMR	IC50:  0.28999999165534973   nM  BindingDB
ZMR	IC50:  7.400000095367432   nM  BindingDB
ZMR	IC50:  0.800000011920929   nM  BindingDB
ZMR	IC50:  1.100000023841858   nM  BindingDB
ZMR	IC50:  0.6000000238418579   nM  BindingDB
ZMR	IC50:  2.700000047683716   nM  BindingDB
ZMR	IC50:  2.200000047683716   nM  BindingDB
ZMR	IC50:  1.600000023841858   nM  BindingDB
ZMR	IC50:  9.199999809265137   nM  BindingDB
ZMR	IC50:  8.699999809265137   nM  BindingDB
ZMR	IC50:  1.2000000476837158   nM  BindingDB
ZMR	IC50:  8.199999809265137   nM  BindingDB
ZMR	IC50:  40   nM  BindingDB
ZMR	IC50:  0.03999999910593033   nM  BindingDB
ZMR	IC50:  45   nM  BindingDB
ZMR	IC50:  34   nM  BindingDB
ZMR	IC50:  7.599999904632568   nM  BindingDB
ZMR	IC50:  0.20000000298023224   nM  BindingDB
ZMR	IC50:  14   nM  BindingDB
ZMR	IC50:  2.4000000953674316   nM  BindingDB
ZMR	IC50:  5.599999904632568   nM  BindingDB
ZMR	IC50:  12   nM  BindingDB
ZMR	IC50:  5.099999904632568   nM  BindingDB
ZMR	IC50:  13   nM  BindingDB
ZMR	IC50:  3.299999952316284   nM  BindingDB
ZMR	IC50:  23   nM  BindingDB
ZMR	IC50:  1.7000000476837158   nM  BindingDB
ZMR	IC50:  2.9000000953674316   nM  BindingDB
ZMR	IC50:  18   nM  BindingDB
ZMR	IC50:  2.299999952316284   nM  BindingDB
ZMR	IC50:  4.300000190734863   nM  BindingDB
ZMR	IC50:  4.800000190734863   nM  BindingDB
ZMR	Ki:  1.600000023841858   nM  BindingDB
ZMR	IC50:  5.800000190734863   nM  BindingDB
ZMR	IC50:  52   nM  BindingDB
ZMR	IC50:  3.4000000953674316   nM  BindingDB
ZMR	IC50:  1.899999976158142   nM  BindingDB
ZMR	IC50:  0.05000000074505806   nM  BindingDB
ZMR	IC50:  8.600000381469727   nM  BindingDB
ZMR	IC50:  9.100000381469727   nM  BindingDB
ZMR	IC50:  3.4000000953674316   nM  BindingDB
ZMR	IC50:  1.399999976158142   nM  BindingDB
ZMR	IC50:  0.4699999988079071   nM  BindingDB
ZMR	IC50:  0.699999988079071   nM  BindingDB
ZMR	IC50:  2.299999952316284   nM  BindingDB
ZMR	IC50:  6.800000190734863   nM  BindingDB
ZMR	IC50:  7.300000190734863   nM  BindingDB
ZMR	IC50:  7.800000190734863   nM  BindingDB
ZMR	IC50:  1.5   nM  BindingDB
ZMR	IC50:  0.800000011920929   nM  BindingDB
ZMR	IC50:  2.200000047683716   nM  BindingDB
ZMR	IC50:  2.5   nM  BindingDB
ZMR	IC50:  2   nM  BindingDB
ZMR	IC50:  0.8799999952316284   nM  BindingDB
ZMR	Ki:  0.4000000059604645   nM  BindingDB
ZMR	IC50:  0.44999998807907104   nM  BindingDB
ZMR	IC50:  0.75   nM  BindingDB
ZMR	Ki:  1   nM  BindingDB
ZMR	IC50:  1   nM  BindingDB
ZMR	IC50:  2.4000000953674316   nM  BindingDB
ZMR	IC50:  6   nM  BindingDB
ZMR	Ki:  0.5   nM  BindingDB
ZMR	IC50:  6.5   nM  BindingDB
ZMR	IC50:  10   nM  BindingDB
ZMR	IC50:  11   nM  BindingDB
ZMR	IC50:  0.6600000262260437   nM  BindingDB
ZMR	IC50:  3.5   nM  BindingDB
ZMR	IC50:  3   nM  BindingDB
ZMR	IC50:  5.5   nM  BindingDB
ZMR	IC50:  12   nM  BindingDB
ZMR	IC50:  4   nM  BindingDB
ZMR	IC50:  1   nM  BindingDB
ZMR	IC50:  3.0999999046325684   nM  BindingDB
ZMR	IC50:  3.5999999046325684   nM  BindingDB
ZMR	IC50:  4.199999809265137   nM  BindingDB
ZMR	IC50:  0.49000000953674316   nM  BindingDB
ZMR	IC50:  5   nM  BindingDB
ZMR	IC50:  0.029999999329447746   nM  BindingDB
ZMR	IC50:  1.7999999523162842   nM  BindingDB
ZMR	IC50:  6.699999809265137   nM  BindingDB
ZMR	IC50:  1.559999942779541   nM  BindingDB
ZMR	IC50:  7.199999809265137   nM  BindingDB
ZMR	IC50:  7.699999809265137   nM  BindingDB
ZMR	IC50:  2   nM  BindingDB
ZMR	IC50:  1.2999999523162842   nM  BindingDB
ZMR	IC50:  1.7999999523162842   nM  BindingDB
ZMR	IC50:  2.0999999046325684   nM  BindingDB
ZMR	IC50:  5.199999809265137   nM  BindingDB
ZMR	IC50:  2.5999999046325684   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 = 118.044	α = 90
b = 129.247	β = 90
c = 118.845	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-10-30 
• Released Date: 2008-10-07 
Deposition Author(s): Xu, X., Zhu, X., Wilson, I.A.

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
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary