6OCB | pdb_00006ocb

Crystal structure of FluA-20 Fab in complex with the head domain of H3 (A/Hong Kong/1/1968)

• PDB DOI: https://doi.org/10.2210/pdb6OCB/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza A virus (A/Hong Kong/1/1968(H3N2))
• Expression System: Homo sapiens, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-03-22 Released: 2019-05-29 
• Deposition Author(s): Wilson, I.A., Lang, S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Models: experimental

Literature

A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface.

Bangaru, S., Lang, S., Schotsaert, M., Vanderven, H.A., Zhu, X., Kose, N., Bombardi, R., Finn, J.A., Kent, S.J., Gilchuk, P., Gilchuk, I., Turner, H.L., Garcia-Sastre, A., Li, S., Ward, A.B., Wilson, I.A., Crowe Jr., J.E.

(2019) Cell 177: 1136-1152.e18

• PubMed: 31100268 
• DOI: https://doi.org/10.1016/j.cell.2019.04.011
• Primary Citation Related Structures: 
  6OBZ, 6OC3, 6OCB


• PubMed Abstract: 
  

  Here, we describe the discovery of a naturally occurring human antibody (Ab), FluA-20, that recognizes a new site of vulnerability on the hemagglutinin (HA) head domain and reacts with most influenza A viruses. Structural characterization of FluA-20 with H1 and H3 head domains revealed a novel epitope in the HA trimer interface, suggesting previously unrecognized dynamic features of the trimeric HA protein. The critical HA residues recognized by FluA-20 remain conserved across most subtypes of influenza A viruses, which explains the Ab's extraordinary breadth. The Ab rapidly disrupted the integrity of HA protein trimers, inhibited cell-to-cell spread of virus in culture, and protected mice against challenge with viruses of H1N1, H3N2, H5N1, or H7N9 subtypes when used as prophylaxis or therapy. The FluA-20 Ab has uncovered an exceedingly conserved protective determinant in the influenza HA head domain trimer interface that is an unexpected new target for anti-influenza therapeutics and vaccines.

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Organizational Affiliation: 
• Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Department of Medicine and Biomedical Sciences, School of Medicine, University of California, San Diego, CA 92093, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].
Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: [e-mail].

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: 79.27 kDa 
• Atom Count: 5,746 
• Modeled Residue Count: 702 
• Deposited Residue Count: 723 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of FluA-20 Fab	A [auth H]	235	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of FluA-20 Fab	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	C [auth A]	274	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7  Go to UniProtKB:  Q91MA7
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [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: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.554	α = 90
b = 84.554	β = 90
c = 271.737	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Wilson, I.A., Lang, S.

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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	R56 AI127371
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI097092
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201400024C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HSN272201400008C
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	No. UL1 TR002243
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	No. HHSN27220170041I

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2020-12-09
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary