8ZDV

The cryoEM structure of H5N8 HA in an auto inhibited state

PDB DOI: https://doi.org/10.2210/pdb8ZDV/pdb
EM Map EMD-60014: EMDB EMDataResource

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

Deposited: 2024-05-03 Released: 2024-09-25
Deposition Author(s): Li, R., Gao, J., Wang, L., Gui, M., Xiang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites

Li, R., Gao, J., Wang, L., Gui, M., Xiang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 186.24 kDa
Atom Count: 12,210
Modelled Residue Count: 1,473
Deposited Residue Count: 1,578
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A [auth B], B [auth A], C	336	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus) Explore A0A8E4ZAK5 Go to UniProtKB: A0A8E4ZAK5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8E4ZAK5
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth B] Focus chain B [auth A] Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	D [auth G], E [auth H], F [auth I]	190	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A8K1DYS3 (Influenza A virus) Explore A0A8K1DYS3 Go to UniProtKB: A0A8K1DYS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8K1DYS3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth G] Focus chain E [auth H] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(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	G [auth D], H [auth E], I [auth F]	7		N-Glycosylation	Interactions Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F] Interactions & Density Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G85526ZL GlyCosmos: G85526ZL GlyGen: G85526ZL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I]	J [auth B] K [auth B] L [auth B] M [auth A] N [auth A] J [auth B], K [auth B], L [auth B], M [auth A], N [auth A], O [auth A], P [auth C], Q [auth C], R [auth C], S [auth G], T [auth H], U [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I]