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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

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

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

(2026) Eur J Immunol

DOI: https://doi.org/10.1002/eji.70158

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab20 heavy chain	A [auth B]	118	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab20 light chain	B [auth A]	107	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29965
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-25

Deposition Author(s):

Kristoffersen, E.L.

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF21OC0070452

Revision History (Full details and data files)

Version 1.0: 2026-02-25
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.