8ZDW | pdb_00008zdw

The cryoEM structure of H5N1 HA split from symmetric filament in conformation A

PDB DOI: https://doi.org/10.2210/pdb8ZDW/pdb
EM Map EMD-60015: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1)), Mus musculus
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: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.4 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.

(2024) Npj Viruses 2: 48-48

PubMed: 40295773 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44298-024-00059-9
Primary Citation Related Structures:
8ZDV, 8ZDW

PubMed Abstract:
The hemagglutinin (HA) glycoprotein of influenza virus binds host cell receptors and mediates viral entry. Here we present cryo-EM structures of fully glycosylated HAs from H5N1 and H5N8 influenza viruses. We find that the H5N1 HA can form filaments that comprise two head-to-head HA trimers. Multivalent interactions between the two HA trimers are mediated by glycans attached to N158. The distal Sia1-Gal2-NAG3 sugar moiety of N158 interacts with the receptor binding site on the opposing HA trimer. Additional interactions are observed between NAG3 and residues K222 and K193. The H5N8 HA lacks the N158 glycosylation site and does not form the filamentous structure. However, the H5N8 HA exhibits an auto-inhibition conformation, where the receptor binding site is occupied by the glycan chain attached to residue N169 from a neighboring protomer. These structures represent native HA-glycan interactions, which may closely mimic the receptor-HA interactions on the cell surface.

Organizational Affiliation

Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, 100084, Beijing, China.

Macromolecule Content

Total Structure Weight: 345.8 kDa
Atom Count: 22,602
Modeled Residue Count: 2,802
Deposited Residue Count: 3,012
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, K [auth C], L [auth H]	337	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DQ33
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain K [auth C] Focus chain L [auth H]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, E [auth D], F [auth I]	228	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DQ33
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain E [auth D] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H5M9 Fab, light chain	C [auth R], I [auth E], J	217	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain	D [auth U], G [auth F], H [auth L]	222	Mus musculus	Mutation(s): 0
UniProt
Find proteins for U5LP42 (Mus musculus) Explore U5LP42 Go to UniProtKB: U5LP42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5LP42
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G], P [auth N], S [auth Q]	2		N-Glycosylation	Interactions Focus chain M [auth G] Focus chain P [auth N] Focus chain S [auth Q] Interactions & Density Focus chain M [auth G] Focus chain P [auth N] Focus chain S [auth Q]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N [auth K], O [auth M], Q [auth O], R [auth P], T [auth S], N [auth K], O [auth M], Q [auth O], R [auth P], T [auth S], U [auth T]	3		N-Glycosylation	Interactions Focus chain N [auth K] Focus chain O [auth M] Focus chain Q [auth O] Focus chain R [auth P] Focus chain T [auth S] Focus chain U [auth T] Interactions & Density Focus chain N [auth K] Focus chain O [auth M] Focus chain Q [auth O] Focus chain R [auth P] Focus chain T [auth S] Focus chain U [auth T]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	V, W, X	3		N/A	Interactions Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

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 AA [auth B] SDF format, chain BA [auth R] SDF format, chain IA [auth H] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain JA [auth H] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth J] SDF format, chain EA [auth E] SDF format, chain DA [auth I] SDF format, chain CA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth R] MOL2 format, chain IA [auth H] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth R] mmCIF format, chain IA [auth H] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth D]	AA [auth B] BA [auth R] CA [auth D] DA [auth I] EA [auth E] AA [auth B], BA [auth R], CA [auth D], DA [auth I], EA [auth E], FA [auth J], GA [auth C], HA [auth C], IA [auth H], JA [auth H], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth R] Focus chain CA [auth D] Focus chain DA [auth I] Focus chain EA [auth E] Focus chain FA [auth J] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth R] Focus chain CA [auth D] Focus chain DA [auth I] Focus chain EA [auth E] Focus chain FA [auth J] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain Y [auth A] Focus chain Z [auth A]