9D2M | pdb_00009d2m

Map of hemagglutinin A/Sing/INFIMH/16 expressed in 293F cells

PDB DOI: https://doi.org/10.2210/pdb9D2M/pdb
EM Map EMD-46500: EMDB EMDataResource

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

Deposited: 2024-08-08 Released: 2025-08-13
Deposition Author(s): Torrents de la Pena, A., Ward, A.B., de Paiva Froes Rocha, R.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift

de Paiva Froes Rocha, R., Torrents de la Pena, A., Ward, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 288.94 kDa
Atom Count: 12,090
Modeled Residue Count: 1,434
Deposited Residue Count: 2,478
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	826	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A2R4U2X2 (Influenza A virus) Explore A0A2R4U2X2 Go to UniProtKB: A0A2R4U2X2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2R4U2X2
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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, F, H, J, L D, F, H, J, L, N	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain H Focus chain J Focus chain L Focus chain N Interactions & Density Focus chain D Focus chain F Focus chain H Focus chain J Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, K, M E, G, I, K, M, O	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain I Focus chain K Focus chain M Focus chain O Interactions & Density Focus chain E Focus chain G Focus chain I Focus chain K Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 B] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth B] 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 B] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth B] 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 B] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth C] EA [auth C] AA [auth B], BA [auth B], CA [auth B], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth B], 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 B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] 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 B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]