8ZDW

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 1.0 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: 345.8 kDa
Atom Count: 22,602
Modelled Residue Count: 2,802
Deposited Residue Count: 3,012
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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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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% Identity50% Identity70% Identity90% Identity95% Identity100% 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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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth R] Focus chain I [auth E] Focus chain J
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5LP42
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]

Entity ID: 6
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	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]

Entity ID: 7
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	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

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 CA [auth D] SDF format, chain DA [auth I] SDF format, chain EA [auth E] SDF format, chain FA [auth J] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth R] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	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]