Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Cyclic - C4  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A8B4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 392.14 kDa 
• Atom Count: 19992 
• Residue Count: 2504 
• Unique protein chains: 3

6PZY

CryoEM derived model of NA-73 Fab in complex with N9 Shanghai2

• DOI: 10.2210/pdb6PZY/pdb
• EMDataResource: EMD-20540

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9)), Homo sapiens
• Expression System: Spodoptera frugiperda, Cricetinae gen. sp.
• Mutation(s): No 


• Deposited: 2019-08-01 Released: 2019-12-04 
• Deposition Author(s): Ward, A.B., Turner, H.L., Zhu, X.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.

Zhu, X., Turner, H.L., Lang, S., McBride, R., Bangaru, S., Gilchuk, I.M., Yu, W., Paulson, J.C., Crowe Jr., J.E., Ward, A.B., Wilson, I.A.

(2019) Cell Host Microbe 26: 729

• PubMed: 31757767 
• DOI: 10.1016/j.chom.2019.10.002
• Primary Citation of Related Structures:  
  6U02, 6PZY, 6PZZ, 6PZW, 6PZH, 6PZE, 6PZD, 6PZG, 6PZF


• PubMed Abstract: 
  

Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B, E, F	429	Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
Find proteins for S5MF06 (Influenza A virus) Explore S5MF06  Go to UniProtKB:  S5MF06

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NA-73 fragment antibody heavy chain	C, G, H, I	232	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NA-73 fragment antibody light chain	D, J, K, L	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O, Q, S	9		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, P, R, T	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-01 
• Released Date: 2019-12-04 
Deposition Author(s): Ward, A.B., Turner, H.L., Zhu, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI117905
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN 272201400024C

Revision History 

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary