9I5N: Fab20 heavy chain

Single particle cryo electron microscopy of a Fab fragment bound to recombinant human CD40 ligand. Determined by electron microscopy at 3.4 Å resolution. Released 25 Feb 2026.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 2,833
Mol. weight: 40.13 kDa
Ligands: MG
Released: 25 Feb 2026

Explore 9I5N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I5N contains 8 α-helices and 38 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
α-helix	18	1
β-strand	19-25	7	6
β-strand	34-38	5	7
β-strand	45-48	4	7
α-helix	53	1
β-strand	54	1	7
α-helix	55	1
β-strand	62-66	5	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-89	5	7
α-helix	96	1
β-strand	102-106	5	7

Chain B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	6-7	2	2
β-strand	11	1	3
β-strand	16	1	4
β-strand	19-23	5	2
β-strand	25	1	1
β-strand	34-40	7	5
β-strand	44-47	4	5
α-helix	61-63	3
β-strand	68-72	5	2
β-strand	77-81	5	2
β-strand	85	1	4
α-helix	87-89	3
β-strand	91-98	8	5
β-strand	107-110	4	5
α-helix	111-113	3
β-strand	114-116	3	5
β-strand	117	1	3

Chain C: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	8
β-strand	137	1	9
β-strand	140-141	2	8
β-strand	147-148	2	8
β-strand	153-156	4	9
β-strand	160-163	4	9
β-strand	167-179	13	8
β-strand	189-196	8	9
β-strand	207-210	4	9
β-strand	219-231	13	8
β-strand	236-241	6	9
β-strand	247	1	8
β-strand	255-260	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab20 heavy chain	B	protein	118	Mus musculus
Fab20 light chain	A	protein	107	Mus musculus
CD40 ligand, soluble form	C	protein	143	Homo sapiens	P29965 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9I5N_1 Fab20 heavy chain (chains B)
QVQLKQSGPGLVQPSQSLSITCTVSGFSLTGYGVHWVRQSPGKGLEWLGMIWSGGSTDYN
AAFISRLSISKDSSKSQVFFKMNSLQANDTAIYYCARSSGNYGEDAMDYWGQGTSVTV

Sequence of entity 2 (A), FASTA

>9I5N_2 Fab20 light chain (chains A)
ETTVTQSPASLSMAIGEKVTIRCITSTDIDDDMNWYQQKPGEPPELLISEDNTLRPGVPS
RFSSSGYGTDFVFAIENMLPEDVADYFCLQSDNLPFTFGSGTKLEIK

Sequence of entity 3 (C), FASTA

>9I5N_3 CD40 ligand, soluble form (chains C)
NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFC
SNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVF
VNVTDPSQVSHGTGFTSFGLLKL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Curbing Autoimmunity: A New Fab Fragment Targeting CD40-CD40L Halts B-Cell Activation and Differentiation. Pedersen, K., Green, K., Kristoffersen, E.L. et al. Eur J Immunol (2026) 56:e70158-e70158. DOI 10.1002/eji.70158 · PubMed

Other PDB entries of the same protein (UniProt P29965 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W9G 1.82 Å, Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the…
1ALY 2.0 Å, Crystal structure of human CD40 ligand
7SGM 2.0 Å, Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with…
3LKJ 2.5 Å, Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit…
6BRB 2.82 Å, Novel non-antibody protein scaffold targeting CD40L
1I9R 3.1 Å, Structure of CD40L in complex with the FAB fragment of humanized 5C8 antibody
3QD6 3.5 Å, Crystal structure of the CD40 and CD154 (CD40L) complex

Browse structure collections

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