9O8S | pdb_00009o8s

Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)

PDB DOI: https://doi.org/10.2210/pdb9O8S/pdb
EM Map EMD-70235: EMDB EMDataResource

Classification: Viral protein/Immune System
Organism(s): Influenza A virus (A/Hong Kong/485197/2014(H3N2)), Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-04-16 Released: 2026-02-04
Deposition Author(s): Jo, G., 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: 2.65 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

A single amino acid substitution in hemagglutinin stalk drives heterosubtypic imprinting of cross-group reactive B cells in children

Jo, G., Ward, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 283.9 kDa
Atom Count: 17,628
Modeled Residue Count: 2,163
Deposited Residue Count: 2,454
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 HA1	A, E [auth C], I [auth D]	345	Influenza A virus (A/Hong Kong/485197/2014(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A0K0YAS1 (Influenza A virus) Explore A0A0K0YAS1 Go to UniProtKB: A0A0K0YAS1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K0YAS1
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A Focus chain E [auth C] Focus chain I [auth D]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, F [auth E], J [auth F]	236	Influenza A virus (A/Hong Kong/485197/2014(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A0K0YAS1 (Influenza A virus) Explore A0A0K0YAS1 Go to UniProtKB: A0A0K0YAS1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K0YAS1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain F [auth E] Focus chain J [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NI04359_d30_240 Fab heavy chain	C [auth H], G, K [auth I]	130	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NI04359_d30_240 Fab light chain	D [auth L], H [auth J], L [auth K]	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O, R, T, W M, O, R, T, W, Y	2		N-Glycosylation	Interactions Focus chain M Focus chain O Focus chain R Focus chain T Focus chain W Focus chain Y Interactions & Density Focus chain M Focus chain O Focus chain R Focus chain T Focus chain W Focus chain Y

Entity ID: 6
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	N, S, X	3		N-Glycosylation	Interactions Focus chain N Focus chain S Focus chain X Interactions & Density Focus chain N Focus chain S Focus chain X

Entity ID: 7
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	AA [auth a], P, Q, U, V, AA [auth a], P, Q, U, V, Z	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain P Focus chain Q Focus chain U Focus chain V Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain P Focus chain Q Focus chain U Focus chain V Focus chain Z

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 BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth E] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth F] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth F] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth F]	BA [auth A] CA [auth A] DA [auth A] EA [auth A] FA [auth A] BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth B], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth E], NA [auth D], OA [auth D], PA [auth D], QA [auth D], RA [auth D], SA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth E] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth F] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth E] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth F]