9E69 | pdb_00009e69

Antibody 5E10

• PDB DOI: https://doi.org/10.2210/pdb9E69/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-29 Released: 2025-07-16 
• Deposition Author(s): Zhou, T., Sao-Fong Cheung, C., Kwong, P.D.
• 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: 2.63 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody.

Rawi, R., Morano, N.C., Cheung, C.S., Du, H., Gorman, J., Prabhakaran, M., Becker, J.E., Bylund, T., Charaf, S., Chen, X., Lee, M., Harris, D.R., Olia, A.S., Ou, L., Wang, L., Wang, S., Zhang, B., Kanekiyo, M., McDermott, A.B., Zhou, T., Shapiro, L., Kwong, P.D.

(2025) Structure 33: 1820-1830.e4

• PubMed: 40816277 
• DOI: https://doi.org/10.1016/j.str.2025.07.015
• Primary Citation of Related Structures:  
  9E69, 9EI8, 9EI9


• PubMed Abstract: 
  

  The N terminus of the H3 subtype of influenza virus hemagglutinin is ∼10 residues longer than the N termini of most other hemagglutinins. As conserved, exposed, and linear regions may be good vaccine targets, we investigated the vaccine utility of the extended H3-N terminus. First, we identified antibody 5E10, for which structure and binding analyses revealed recognition of the H3-N terminus. Second, we immunized mice with immunogens incorporating the H3-N terminus, boosted with hemagglutinin trimer, and isolated antibodies from immunogen-elicited B cells that bound both H3-N terminus and hemagglutinin trimer. However, hemagglutinin-complex structures of two such antibodies, 3864-6 and 3864-10, that neutralized H3-influenza strains, revealed only peripheral recognition of the hemagglutinin N terminus. Collectively, these results reveal the N terminus of H3 hemagglutinin to be a suboptimal vaccine target and suggest that-in addition to being conserved, flexible, and accessible-other factors influence the elicitation of potent broadly neutralizing responses.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].
Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 99.66 kDa 
• Atom Count: 6,444 
• Modeled Residue Count: 857 
• Deposited Residue Count: 933 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of antibody 5E10	A [auth H]	238	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of antibody 5E10	B [auth L]	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of antibody 5E10	C [auth A]	236	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of antibody 5E10	D [auth B]	230	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.969	α = 90
b = 93.969	β = 90
c = 107.667	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Zhou, T., Sao-Fong Cheung, C., Kwong, P.D.

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

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release
  
• Version 1.1: 2026-01-28
  Changes: Database references
• Version 1.2: 2026-02-04
  Changes: Database references