12IV | pdb_000012iv

CryoEM structure of monoclonal Fab 047-09 1A02 binding the lateral patch of influenza virus H1 HA (A/California/04/2009 H1N1)

PDB DOI: https://doi.org/10.2210/pdb12IV/pdb
EM Map EMD-76462: EMDB EMDataResource

Classification: IMMUNE SYSTEM/Viral Protein
Organism(s): Influenza A virus (A/California/04/2009(H1N1)), Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2026-04-07 Released: 2026-09-23
Deposition Author(s): Fernandez-Quintero, M.L., Han, J., Ward, A.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.76 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

Temporal and cross-species convergence of influenza H1 lateral patch antigenic drift

Fernandez-Quintero, M.L., Han, J., Ward, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 239.75 kDa
Atom Count: 16,831
Modeled Residue Count: 2,124
Deposited Residue Count: 2,124
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	A, B, D	160	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 1 Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1 Go to UniProtKB: C3W5S1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3W5S1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	C, E, F	321	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1 Go to UniProtKB: C3W5S1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3W5S1
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain 1A02	G [auth I], H [auth J], I [auth K]	121	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain 1A02	J [auth R], K [auth P], L [auth Q]	106	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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 O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth E] SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B]	M [auth B] N [auth C] O [auth C] P [auth C] Q [auth C] M [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth E], T [auth E], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth F], Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]