Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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

• PDB 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

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMR	BindingDB:  3B7E	Ki: min: 0.4, max: 1.6 (nM) from 4 assay(s)
		IC50: min: 0.03, max: 52 (nM) from 96 assay(s)

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