7KQI

Antibodies that engage the hemagglutinin receptor-binding site of influenza B viruses

• PDB DOI: https://doi.org/10.2210/pdb7KQI/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Influenza B virus (B/Yamagata/16/1988)
• Expression System: Homo sapiens, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-11-16 Released: 2020-12-16 
• Deposition Author(s): Bajic, G., Harrison, S.C.
• 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: 4.20 Å
• R-Value Free: 0.420 
• R-Value Work: 0.372 
• R-Value Observed: 0.377 

Starting Models: experimental

Literature

Antibodies That Engage the Hemagglutinin Receptor-Binding Site of Influenza B Viruses.

Bajic, G., Harrison, S.C.

(2021) ACS Infect Dis 7: 1-5

• PubMed: 33274930 
• DOI: https://doi.org/10.1021/acsinfecdis.0c00726
• Primary Citation of Related Structures:  
  7KQG, 7KQH, 7KQI


• PubMed Abstract: 
  

  We describe cross-reactive human antibodies recognizing influenza B viruses spanning nearly 80 years of antigenic drift. Structures show that they engage the receptor-binding site (RBS) of the viral hemagglutinin with strong similarities to their influenza A counterparts, despite structural differences between the RBS of influenza A and B. Our data show that these antibodies readily cross-react with both influenza B Victoria and Yamagata lineages. We also note that all antibodies are encoded by IGHV3-9/IGK1-33. Future research will provide insight into the prevalence of these antibodies in the human population.

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Organizational Affiliation: 

Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 83.26 kDa 
• Atom Count: 5,070 
• Modelled Residue Count: 652 
• Deposited Residue Count: 754 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1209 Fab heavy chain	A	240	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1209 Fab light chain	B [auth C]	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	C [auth B]	298	Influenza B virus (B/Yamagata/16/1988)	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P18880 (Influenza B virus (strain B/Yamagata/16/1988)) Explore P18880  Go to UniProtKB:  P18880
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62916OK GlyCosmos:  G62916OK GlyGen:  G62916OK

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.420 
• R-Value Work: 0.372 
• R-Value Observed: 0.377 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.1	α = 90
b = 128.1	β = 90
c = 235.28	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Bajic, G., Harrison, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI089618

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2021-01-20
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary