9GSP | pdb_00009gsp

Structure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin. The 2021 Influenza A(H1N1)pdm09 egg-derived vaccine candidate.

PDB DOI: https://doi.org/10.2210/pdb9GSP/pdb
EM Map EMD-51553: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): H1N1 subtype
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-09-16 Released: 2025-10-08
Deposition Author(s): Waraich, K., Meir, A., Petrov, F., Akbar, S., Smith, T., Anne Scott, K., Dibben, O., Bhella, D.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.68 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 1.0 of the entry. See complete history.

Literature

Structure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin. The 2021 Influenza A(H1N1)pdm09 egg-derived vaccine candidate.

Waraich, K., Meir, A., Petrov, F., Akbar, S., Smith, T., Anne Scott, K., Dibben, O., Bhella, D.

To be published.

Macromolecule Content

Total Structure Weight: 196.34 kDa
Atom Count: 12,000
Modeled Residue Count: 1,464
Deposited Residue Count: 1,698
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	566	H1N1 subtype	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A6M4YP75 (Influenza A virus) Explore A0A6M4YP75 Go to UniProtKB: A0A6M4YP75
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6M4YP75
Glycosylation
Glycosylation Sites: 6	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, I	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain I Interactions & Density Focus chain D Focus chain F Focus chain I
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, H	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain G Focus chain H
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 U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth B] J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth C], S [auth C], T [auth C], U [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]