Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer -A6B3C3 

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 104965.04 
• Atom Count: 7198 
• Residue Count: 945 
• Unique protein chains: 4

5V2A

Crystal structure of Fab H7.167 in complex with influenza virus hemagglutinin from A/Shanghai/02/2013 (H7N9)

• DOI: 10.2210/pdb5V2A/pdb
• Entry 5V2A supersedes 5F45

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus, Influenza A virus
• Expression System: Trichoplusia ni, Homo sapiens


• Deposited: 2017-03-03 Released: 2017-04-05 
• Deposition Author(s): Zhang, H., Zhu, X., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.656 Å
• R-Value Free: 0.334 
• R-Value Work: 0.258 

Literature

H7N9 influenza virus neutralizing antibodies that possess few somatic mutations.

Thornburg, N.J., Zhang, H., Bangaru, S., Sapparapu, G., Kose, N., Lampley, R.M., Bombardi, R.G., Yu, Y., Graham, S., Branchizio, A., Yoder, S.M., Rock, M.T., Creech, C.B., Edwards, K.M., Lee, D., Li, S., Wilson, I.A., Garcia-Sastre, A., Albrecht, R.A., Crowe, J.E.

(2016) J. Clin. Invest. 126: 1482-1494

• PubMed: 26950424 
• DOI: 10.1172/JCI85317
• Primary Citation of Related Structures:  
  5F45


• PubMed Abstract: 
  

Avian H7N9 influenza viruses are group 2 influenza A viruses that have been identified as the etiologic agent for a current major outbreak that began in China in 2013 and may pose a pandemic threat. Here, we examined the human H7-reactive antibody response in 75 recipients of a monovalent inactivated A/Shanghai/02/2013 H7N9 vaccine. After 2 doses of vaccine, the majority of donors had memory B cells that secreted IgGs specific for H7 HA, with dominant responses against single HA subtypes, although frequencies of H7-reactive B cells ranged widely between donors. We isolated 12 naturally occurring mAbs with low half-maximal effective concentrations for binding, 5 of which possessed neutralizing and HA-inhibiting activities. The 5 neutralizing mAbs exhibited narrow breadth of reactivity with influenza H7 strains. Epitope-mapping studies using neutralization escape mutant analysis, deuterium exchange mass spectrometry, and x-ray crystallography revealed that these neutralizing mAbs bind near the receptor-binding pocket on HA. All 5 neutralizing mAbs possessed low numbers of somatic mutations, suggesting the clones arose from naive B cells. The most potent mAb, H7.167, was tested as a prophylactic treatment in a mouse intranasal virus challenge study, and systemic administration of the mAb markedly reduced viral lung titers.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin	A	321	Influenza A virus	Mutation(s): 0  Gene Names: HA
Find proteins for A0A0R5TXT5 (Influenza A virus) Go to UniProtKB:  A0A0R5TXT5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin	B	183	Influenza A virus	Mutation(s): 0  Gene Names: HA
Find proteins for A0A097PHH8 (Influenza A virus) Go to UniProtKB:  A0A097PHH8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Light chain (kappa) of H7.167 antibody	L	221	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Heavy chain of H7.167 antibody	H	220	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BMA	H	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, H	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.656 Å
• R-Value Free: 0.334 
• R-Value Work: 0.258 
• Space Group: I 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 207.276	α = 90.00
b = 207.276	β = 90.00
c = 207.276	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-03 
• Released Date: 2017-04-05 
• Deposition Author(s): Zhang, H., Zhu, X., Wilson, I.A.
• This entry supersedes: 5F45

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	R56 AI117675

Revision History 

• Version 1.0: 2017-04-05
  Type: Initial release
• Version 1.1: 2017-07-05
  Type: Source and taxonomy
• Version 1.2: 2017-09-06
  Type: Author supporting evidence
• Version 1.3: 2018-03-07
  Type: Source and taxonomy