9I5N | pdb_00009i5n

Single particle cryo electron microscopy of a Fab fragment bound to recombinant human CD40 ligand

• PDB DOI: https://doi.org/10.2210/pdb9I5N/pdb
• EM Map EMD-52634: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-28 Released: 2026-02-25 
• Deposition Author(s): Kristoffersen, E.L., Schinkel, T., Andersen, E.S.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Curbing Autoimmunity: A New Fab Fragment Targeting CD40-CD40L Halts B-Cell Activation and Differentiation.

Pedersen, K., Green, K., Kristoffersen, E.L., Schinkel, T., Hansen, A.G., Palarasah, Y., Rovsing, A.B., Andersen, E.S., Valero, J., Civit, L., Laursen, N.S., Troldborg, A., Degn, S.E., Thiel, S.

(2026) Eur J Immunol 56: e70158-e70158

• PubMed: 41742604 
• DOI: https://doi.org/10.1002/eji.70158
• Primary Citation Related Structures: 
  9I5N


• PubMed Abstract: 
  

  Dysregulation of the CD40-CD40L axis is implicated in autoimmune diseases. Early clinical trials targeting CD40L with antibodies failed due to Fc-mediated side effects. To address this, we developed an anti-CD40L Fab fragment, Fab20, designed to block B-cell activation. Fab20 was evaluated for its binding properties, CD40-CD40L inhibition, and effects on human B-cell activation and differentiation using immunoassays, cryo-electron microscopy, flow cytometry, and cell cultures. Fab20 binds CD40L with a dissociation constant of 70 nM. Structural analysis revealed a "propeller-like" structure consisting of three Fabs binding to the CD40L trimer, sterically blocking parts of the CD40 binding site. Fab20 effectively inhibited B-cell activation, maintaining naïve B cells in their inactive state, and suppressed antibody (IgG) production over 14 days. Fab20 represents a promising novel therapeutic approach for treating autoimmune diseases driven by CD40-CD40L dysregulation. Its mechanism of action, coupled with the absence of Fc-mediated effects, suggests a favorable safety profile.

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Organizational Affiliation: 
• Department of Biomedicine, Aarhus University, Aarhus, Denmark.
Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.
Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
New York Genome Center, New York City, New York, USA.
Department of Biology, New York University, New York City, New York, USA.
Commit Biologics, Aarhus, Denmark.
Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark.
Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 40.13 kDa 
• Atom Count: 2,833 
• Modeled Residue Count: 368 
• Deposited Residue Count: 368 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab20 heavy chain	A [auth B]	118	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab20 light chain	B [auth A]	107	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CD40 ligand, soluble form	C	143	Homo sapiens	Mutation(s): 0  Gene Names: CD40LG, CD40L, TNFSF5, TRAP
UniProt & NIH Common Fund Data Resources
Find proteins for P29965 (Homo sapiens) Explore P29965  Go to UniProtKB:  P29965
PHAROS:  P29965 GTEx:  ENSG00000102245

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Kristoffersen, E.L., Schinkel, T., Andersen, E.S.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF21OC0070452

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release
  
• Version 1.1: 2026-03-11
  Changes: Data collection, Database references