9BDF | pdb_00009bdf

Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85666

PDB DOI: https://doi.org/10.2210/pdb9BDF/pdb
EM Map EMD-44451: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus, Homo sapiens
Expression System: Spodoptera frugiperda, Homo sapiens
Mutation(s): No

Deposited: 2024-04-11 Released: 2024-11-13
Deposition Author(s): Ferreira Ramos, A.S., Bajic, G.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.01 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Conserved sites on the influenza H1 and H3 hemagglutinin recognized by human antibodies.

Maurer, D.P., Vu, M., Ferreira Ramos, A.S., Dugan, H.L., Khalife, P., Geoghegan, J.C., Walker, L.M., Bajic, G., Schmidt, A.G.

(2025) Sci Adv 11: eadu9140-eadu9140

PubMed: 40267182 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adu9140
Primary Citation Related Structures:
9BDF, 9BDG

PubMed Abstract:
Monoclonal antibodies (mAbs) targeting the influenza hemagglutinin (HA) can be used as prophylactics or templates for next-generation vaccines. Here, we isolated broad, subtype-neutralizing mAbs from human B cells recognizing the H1 or H3 HA "head" and a mAb engaging the conserved stem. The H1 mAbs bind the lateral patch epitope on HAs from 1933 to 2021 and a prepandemic swine H1N1 virus. We improved neutralization potency using directed evolution toward a contemporary H1 HA. Deep mutational scanning of four antigenically distinct H1N1 viruses identified potential viral escape pathways. For the H3 mAbs, we used cryo-electron microscopy to define their epitopes: One mAb binds the side of the HA head, accommodating the N133 glycan and a pocket underneath the receptor binding site; the other mAb recognizes an HA stem epitope that partially overlaps with previously characterized mAbs but with distinct antibody variable genes. Collectively, these mAbs identify conserved sites recognized by broadly-reactive mAbs that may be elicited by next-generation vaccines.

Organizational Affiliation

Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA.

Macromolecule Content

Total Structure Weight: 327.9 kDa
Atom Count: 17,167
Modeled Residue Count: 2,126
Deposited Residue Count: 2,904
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, F [auth G], G [auth H]	514	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A8F5JT24 (Influenza A virus) Explore A0A8F5JT24 Go to UniProtKB: A0A8F5JT24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8F5JT24
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain F [auth G] Focus chain G [auth H]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADI-85666 Fab heavy chain	B, C, E	240	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ADI-85666 Fab light chain	D, H [auth I], I [auth J]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F], M, R	4		N-Glycosylation	Interactions Focus chain J [auth F] Focus chain M Focus chain R Interactions & Density Focus chain J [auth F] Focus chain M Focus chain R
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	K, N, O, P, Q	2		N-Glycosylation	Interactions Focus chain K Focus chain N Focus chain O Focus chain P Focus chain Q Interactions & Density Focus chain K Focus chain N Focus chain O Focus chain P Focus chain 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	L	3		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth G] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain FA [auth H] SDF format, chain EA [auth H] SDF format, chain DA [auth H] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth G] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth G] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] CA [auth G] DA [auth H] EA [auth H] AA [auth G], BA [auth G], CA [auth G], DA [auth H], EA [auth H], FA [auth H], GA [auth H], HA [auth H], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth G], Y [auth G], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]