9MQ2 | pdb_00009mq2

Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12G1

PDB DOI: https://doi.org/10.2210/pdb9MQ2/pdb
EM Map EMD-48511: EMDB EMDataResource

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

Deposited: 2025-01-01 Released: 2025-11-05
Deposition Author(s): Leon, A.N., Brouwer, P.J.M., Rodriguez, A.J., Han, J., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 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

Human Monoclonal Antibodies that Target Clade 2.3.4.4b H5N1 Hemagglutinin

Pena Alzua, G., Leon, A.N., Brouwer, P.J.M., Yellin, T., Bhavsar, D., Loganathan, M., Bushfield, K., Marizzi, C., Rodriguez, A.J., Han, J., Webby, R., Ward, A.B., Duty, J.A., Florian, K.

To be published.

Macromolecule Content

Total Structure Weight: 223.07 kDa
Atom Count: 13,312
Modeled Residue Count: 1,640
Deposited Residue Count: 1,928
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, B, C	345	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 Focus chain B 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
12G1 Heavy Chain Fab	D [auth H]	122	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
12G1 Light Chain Fab	E [auth L]	111	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	F [auth a], G [auth b], H [auth c]	220	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0AAX6NNL9 (Influenza A virus) Explore A0AAX6NNL9 Go to UniProtKB: A0AAX6NNL9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAX6NNL9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain F [auth a] Focus chain H [auth c]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth D], J [auth E], K [auth F]	3		N-Glycosylation	Interactions Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth F] Interactions & Density Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth F]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

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