9MER | pdb_00009mer

Structure of H1H5:FluA20 Chimeric Influenza HA Complex

PDB DOI: https://doi.org/10.2210/pdb9MER/pdb

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

Deposited: 2024-12-08 Released: 2025-03-19
Deposition Author(s): Seraj, N.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity.

Castro, K.M., Ayardulabi, R., Wehrle, S., Cui, H., Georgeon, S., Schmidt, J., Xiao, S., Seraj, N., Harshbarger, W., Mallett, C.P., Vassilev, V., Saelens, X., Correia, B.E.

(2025) bioRxiv

PubMed: 40027756 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1101/2024.12.17.628867
Primary Citation of Related Structures:
9MER, 9MEV

PubMed Abstract:
Antigenic variability among influenza virus strains poses a significant challenge to developing broadly protective, long-lasting vaccines. Current annual vaccines target specific strains, requiring accurate prediction for effective neutralization. Despite sequence diversity across phylogenetic groups, the hemagglutinin (HA) head domain's structure remains highly conserved. Utilizing this conservation, we designed cross-group chimeric HAs that combine antigenic surfaces from distant strains. By structure-guided transplantation of receptor-binding site (RBS) residues, we displayed an H3 RBS on an H1 HA scaffold. These chimeric immunogens elicit cross-group polyclonal responses capable of neutralizing both base and distal strains. Additionally, the chimeras integrate heterotrimeric immunogens, enhancing modular vaccine design. This approach enables the inclusion of diverse strain segments to generate broad polyclonal responses. In the future, such modular immunogens may serve as tools for evaluating immunodominance and refining immunization strategies, offering potential to bridge and enhance immune responses in individuals with pre-existing immunity. This strategy holds promise for advancing universal influenza vaccine development.

Organizational Affiliation

Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

Macromolecule Content

Total Structure Weight: 76.48 kDa
Atom Count: 5,706
Modeled Residue Count: 655
Deposited Residue Count: 676
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H1H5 HA	A [auth B]	227	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for C8YR92 (Influenza A virus) Explore C8YR92 Go to UniProtKB: C8YR92
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C8YR92
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth B]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FluA20 Heavy Chain Fab	B [auth H]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FluA20 Light Chain Fab	C [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain BA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	BA [auth H], O [auth B], P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain BA [auth H] Focus chain O [auth B] Focus chain P [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain DA [auth L] SDF format, chain E [auth B] SDF format, chain EA [auth L] SDF format, chain F [auth B] SDF format, chain FA [auth L] SDF format, chain G [auth B] SDF format, chain GA [auth L] SDF format, chain H [auth B] SDF format, chain HA [auth L] SDF format, chain I [auth B] SDF format, chain IA [auth L] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth H] SDF format, chain Z [auth H] SDF format, chain N [auth B] SDF format, chain AA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth L] MOL2 format, chain E [auth B] MOL2 format, chain EA [auth L] MOL2 format, chain F [auth B] MOL2 format, chain FA [auth L] MOL2 format, chain G [auth B] MOL2 format, chain GA [auth L] MOL2 format, chain H [auth B] MOL2 format, chain HA [auth L] MOL2 format, chain I [auth B] MOL2 format, chain IA [auth L] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth H] MOL2 format, chain N [auth B] MOL2 format, chain AA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth L] mmCIF format, chain E [auth B] mmCIF format, chain EA [auth L] mmCIF format, chain F [auth B] mmCIF format, chain FA [auth L] mmCIF format, chain G [auth B] mmCIF format, chain GA [auth L] mmCIF format, chain H [auth B] mmCIF format, chain HA [auth L] mmCIF format, chain I [auth B] mmCIF format, chain IA [auth L] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth H] mmCIF format, chain Z [auth H] mmCIF format, chain N [auth B] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth H] DA [auth L] E [auth B] EA [auth L] AA [auth H], CA [auth H], DA [auth L], E [auth B], EA [auth L], F [auth B], FA [auth L], G [auth B], GA [auth L], H [auth B], HA [auth L], I [auth B], IA [auth L], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], Q [auth B], R [auth B], S [auth B], Y [auth H], Z [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth H] Focus chain DA [auth L] Focus chain E [auth B] Focus chain EA [auth L] Focus chain F [auth B] Focus chain FA [auth L] Focus chain G [auth B] Focus chain GA [auth L] Focus chain H [auth B] Focus chain HA [auth L] Focus chain I [auth B] Focus chain IA [auth L] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth H] Focus chain DA [auth L] Focus chain E [auth B] Focus chain EA [auth L] Focus chain F [auth B] Focus chain FA [auth L] Focus chain G [auth B] Focus chain GA [auth L] Focus chain H [auth B] Focus chain HA [auth L] Focus chain I [auth B] Focus chain IA [auth L] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth H] Focus chain Z [auth H]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain JA [auth L] SDF format, chain KA [auth L] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth L] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain JA [auth L] mmCIF format, chain KA [auth L] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	JA [auth L] KA [auth L] T [auth B] U [auth B] V [auth B] JA [auth L], KA [auth L], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain JA [auth L] Focus chain KA [auth L] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain JA [auth L] Focus chain KA [auth L] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]