7KQI | pdb_00007kqi

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 (Depositor), 0.424 (DCC) 
• R-Value Work: 
  0.372 (Depositor), 0.373 (DCC) 
• R-Value Observed: 
  0.377 (Depositor) 

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 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.
Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States.
Howard Hughes Medical Institute, 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 
• Modeled 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	D 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	D 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 (Depositor), 0.424 (DCC) 
• R-Value Work:  0.372 (Depositor), 0.373 (DCC) 
• R-Value Observed: 0.377 (Depositor) 

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