8PK3

CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus bound to an Affimer reagent

• PDB DOI: https://doi.org/10.2210/pdb8PK3/pdb
• EM Map EMD-17724: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Influenza A virus, synthetic construct
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-24 Released: 2024-01-03 
• Deposition Author(s): Debski-Antoniak, O., Flynn, A., Klebl, D.P., Tiede, C., Muench, S., Tomlinson, D., Fontana, J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Exploiting the Affimer platform against influenza A virus

Debski-Antoniak, O., Flynn, A., Klebl, D.P., Tiede, C., Muench, S., Tomlinson, D., Fontana, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 203.49 kDa 
• Atom Count: 14,277 
• Modelled Residue Count: 1,752 
• Deposited Residue Count: 1,752 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, D [auth B], G [auth C]	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B [auth D], E, H [auth F]	175	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Affimer molecule (A31)	C [auth G], F [auth H], I	87	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

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	J, L [auth S], N [auth b]	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	K [auth N], M [auth W], O [auth f]	5	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth A], Q [auth A], R [auth B], S [auth B], T [auth C], U [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): Debski-Antoniak, O., Flynn, A., Klebl, D.P., Tiede, C., Muench, S., Tomlinson, D., Fontana, J.

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Funding Organization	Location	Grant Number
Wellcome Trust		Springboard Award

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release