9EI8 | pdb_00009ei8

Cryo-EM structure of 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer

PDB DOI: https://doi.org/10.2210/pdb9EI8/pdb
EM Map EMD-48078: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Influenza A virus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-11-25 Released: 2025-08-06
Deposition Author(s): Gorman, J., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

PubMed: 40816277 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2025.07.015
Primary Citation 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.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: reda.rawi@nih.gov.

Macromolecule Content

Total Structure Weight: 202.54 kDa
Atom Count: 12,473
Modeled Residue Count: 1,491
Deposited Residue Count: 1,698
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, B, D	334	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A1L6ZD23 (Influenza A virus) Explore A0A1L6ZD23 Go to UniProtKB: A0A1L6ZD23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L6ZD23
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	C, E, F	232	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A7G3K3M3 (Influenza A virus) Explore A0A7G3K3M3 Go to UniProtKB: A0A7G3K3M3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7G3K3M3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
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	G, H, J, L, M G, H, J, L, M, O, P, S	3		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain J Focus chain L Focus chain M Focus chain O Focus chain P Focus chain S Interactions & Density Focus chain G Focus chain H Focus chain J Focus chain L Focus chain M Focus chain O Focus chain P Focus chain S
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, K, N, Q, R	2		N-Glycosylation	Interactions Focus chain I Focus chain K Focus chain N Focus chain Q Focus chain R Interactions & Density Focus chain I Focus chain K Focus chain N Focus chain Q Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain JA [auth F] SDF format, chain IA [auth E] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth C] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain IA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain IA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth C] DA [auth D] EA [auth D] AA [auth B], BA [auth B], CA [auth C], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], IA [auth E], JA [auth F], T [auth A], U [auth A], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]