9O8T | pdb_00009o8t

Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)

• PDB DOI: https://doi.org/10.2210/pdb9O8T/pdb
• EM Map EMD-70236: EMDB EMDataResource

• Classification: Viral protein/Immune System
• Organism(s): Influenza A virus (A/Michigan/45/2015(H1N1)), 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 275.23 kDa 
• Atom Count: 17,142 
• Modeled Residue Count: 2,169 
• Deposited Residue Count: 2,442 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, E [auth C], I [auth D]	344	Influenza A virus (A/Michigan/45/2015(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A1J0CXU0 (Influenza A virus) Explore A0A1J0CXU0  Go to UniProtKB:  A0A1J0CXU0
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, F [auth E], J [auth F]	233	Influenza A virus (A/Michigan/45/2015(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A1J0CXU0 (Influenza A virus) Explore A0A1J0CXU0  Go to UniProtKB:  A0A1J0CXU0
Glycosylation
Glycosylation Sites: 1

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 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

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, N, O	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth A], Q [auth A], R [auth B], S [auth C], T [auth C], U [auth E], V [auth D], W [auth D], X [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Jo, G., Ward, A.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93019C00051

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release