9BU8

Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer

• PDB DOI: https://doi.org/10.2210/pdb9BU8/pdb
• EM Map EMD-44903: EMDB EMDataResource

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


• Deposited: 2024-05-16 Released: 2024-11-27 
• Deposition Author(s): Gorman, J., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.96 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Human vaccination with different group 2 influenza subtypes alters epitope targeting and breadth of hemagglutinin stem-specific B cells

Gorman, J., Kwong, P.D.

(2024) Sci Transl Med 

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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 263.98 kDa 
• Atom Count: 17,109 
• Modelled Residue Count: 2,175 
• Deposited Residue Count: 2,349 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, E, J	325	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A059T4A1 (Influenza A virus) Explore A0A059T4A1  Go to UniProtKB:  A0A059T4A1
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, G, L	230	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A0B4UV34 (Influenza A virus) Explore A0A0B4UV34  Go to UniProtKB:  A0A0B4UV34
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab c115.131 heavy chain	C, F, I	121	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab c115.131 light chain	D, H, K	107	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
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	M, N, O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.96 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5278

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Gorman, J., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103310
Simons Foundation	United States	SF349247

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release