Biological Assembly 1  

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

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)

Macromolecule Content

• Total Structure Weight: 104.93 kDa 
• Atom Count: 7198 
• Modelled Residue Count: 922 
• Deposited 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)

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

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/chicken/Henan/109/2013(H7N9)), Influenza A virus (A/pigeon/Wuxi/0405007G/2013(H7N9)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• 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 (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.66 Å
• R-Value Free: 0.334 
• R-Value Work: 0.258 
• R-Value Observed: 0.261 

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:  
  5V2A


• 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.

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Organizational Affiliation: 

Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	321	Influenza A virus (A/chicken/Henan/109/2013(H7N9))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A0R5TXT5 (Influenza A virus) Explore A0A0R5TXT5  Go to UniProtKB:  A0A0R5TXT5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	183	Influenza A virus (A/pigeon/Wuxi/0405007G/2013(H7N9))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A097PHH8 (Influenza A virus) Explore A0A097PHH8  Go to UniProtKB:  A0A097PHH8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain (kappa) of H7.167 antibody	C [auth L]	221	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of H7.167 antibody	D [auth H]	220	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.66 Å
• R-Value Free: 0.334 
• R-Value Work: 0.258 
• R-Value Observed: 0.261 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.276	α = 90
b = 207.276	β = 90
c = 207.276	γ = 90

Software Package:

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

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 (NIH/NIAID)	United States	R56 AI117675

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Source and taxonomy
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2018-03-07
  Changes: Source and taxonomy
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary