9YOI | pdb_00009yoi

Crystal structure of H3 hemagglutinin with HA2 N95L mutation from the influenza virus A/Hong Kong/1/1968 (H3N2)

PDB DOI: https://doi.org/10.2210/pdb9YOI/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2025-10-13 Released: 2026-08-26
Deposition Author(s): Zhu, X., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.224 (Depositor), 0.222 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: 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

Single-component self-assembling protein nanoparticles displaying stabilized prefusion-closed hemagglutinin trimers for influenza vaccine development

Zhang, Y.N., Zhu, X., Braz Gomes, K., Lee, Y.Z., DesRoberts, C., He, L., Wilson, I.A., Zhu, J.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-76731-w

Macromolecule Content

Total Structure Weight: 179.01 kDa
Atom Count: 12,133
Modeled Residue Count: 1,489
Deposited Residue Count: 1,554
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A [auth C], C [auth A], E	322	Influenza A virus	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91MA7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth C] Focus chain C [auth A] Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B [auth D], D [auth B], F	196	Influenza A virus	Mutation(s): 1 Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7 Go to UniProtKB: Q91MA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91MA7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G

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	H, K	2		N-Glycosylation	Interactions Focus chain H Focus chain K Interactions & Density Focus chain H Focus chain K

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	5		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	6		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J

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 R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C]	L [auth C] M [auth C] N [auth C] O [auth A] P [auth A] L [auth C], M [auth C], N [auth C], O [auth A], P [auth A], Q [auth E], R [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth E] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.224 (Depositor), 0.222 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.844	α = 90
b = 114.156	β = 90
c = 235.332	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Zhu, X.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93021C00015
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI150885