9HJ9 | pdb_00009hj9

H1-H3 chimeric hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb9HJ9/pdb

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

Deposited: 2024-11-28 Released: 2025-12-10
Deposition Author(s): Seraj, N., Harshbarger, W., Mallett, C.P., Vassilev, V.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Models: experimental, in silico
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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 hemagglutinins to elicit cross-group immunity

Castro, K., Ayaradulabi, R., Wehrle, S., Cui, H., Georgon, S., Schmidt, J., Xiao, S., Seraj, N., Harshbarger, W., Mallet, C.P., Vassilev, V., Saelens, X., Correia, B.E.

To be published.

Macromolecule Content

Total Structure Weight: 76.06 kDa
Atom Count: 5,637
Modeled Residue Count: 653
Deposited Residue Count: 686
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A [auth B]	227	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7Y8A2 (Influenza A virus) Explore A7Y8A2 Go to UniProtKB: A7Y8A2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7Y8A2
Glycosylation
Glycosylation Sites: 2	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
FluA-20 fab heavy chain	B [auth C]	237	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FluA-20 fab light chain	C [auth D]	222	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D]	H [auth C], I [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain H [auth C] Focus chain I [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]