Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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: 86792.53 
• Atom Count: 6095 
• 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 (strain A/Brevig Mission/1/1918 H1N1)
• Expression System: Trichoplusia ni


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

---

Experimental Data Snapshot

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

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:  
  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.

---

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
Molecule	Chains	Sequence Length	Organism	Details
Neuraminidase	A, B	385	Influenza 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
FUC	B	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
ZMR	A, B	ZANAMIVIR MODIFIED SIALIC ACID C12 H20 N4 O7 ARAIBEBZBOPLMB-UFGQHTETSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZMR	IC50: 0.5 - 5 nM (93) BINDINGDB
ZMR	Ki: 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 = 118.044	α = 90.00
b = 129.247	β = 90.00
c = 118.845	γ = 90.00

Software Package:

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

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
  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