8X2F | pdb_00008x2f

Cryo-EM structure of H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with Sialyl-Lewis X

PDB DOI: https://doi.org/10.2210/pdb8X2F/pdb
EM Map EMD-38008: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus
Expression System: Baculovirus transfer vector pFASTBAC1
Mutation(s): No

Deposited: 2023-11-09 Released: 2025-05-14
Deposition Author(s): Jin, X.Y., Han, P., Song, H., Qi, J.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8X2F

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

Literature

Enhanced binding of Sialyl Lewis X to hemagglutinin contributes to H5N8 mammalian pathogenicity and infectivity

Jin, X., Han, P., Zhang, C., Maio, A.D., Shi, Y., Qi, J., Bi, Y., Liu, Y., Song, H., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 178.35 kDa
Atom Count: 12,112
Modeled Residue Count: 1,472
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A [auth B], B [auth E], C [auth F]	506	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8E4ZAK5
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth B] Focus chain B [auth E] Focus chain C [auth F]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A], F [auth D], H	4		N/A	Interactions Focus chain D [auth A] Focus chain F [auth D] Focus chain H Interactions & Density Focus chain D [auth A] Focus chain F [auth D] Focus chain H
Glycosylation Resources
GlyTouCan: G00054MO GlyCosmos: G00054MO GlyGen: G00054MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], G, I	2		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain G Focus chain I Interactions & Density Focus chain E [auth C] Focus chain G Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 E] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth F]	J [auth B] K [auth B] L [auth B] M [auth E] N [auth E] J [auth B], K [auth B], L [auth B], M [auth E], N [auth E], O [auth F], P [auth F]	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 E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82122040

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release
Version 1.1: 2025-06-18
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.