7P3I: Human CD40/TNFRSF5

Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein. Determined by X-ray diffraction at 2.29 Å resolution. Released 6 Apr 2022.

Method: X-ray diffraction
Resolution: 2.29 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 5,104
Mol. weight: 72.84 kDa
Released: 6 Apr 2022

Explore 7P3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P3I contains 50 α-helices and 40 β-strands across 4 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.

Chains A and C: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
β-strand	36-39	4	1
α-helix	40	1
β-strand	41	1	2
α-helix	42	1
β-strand	45-49	5	3
α-helix	56-57	2
β-strand	58-61	4	3
α-helix	62-63	2
β-strand	66-67	2	4
β-strand	72	1	2
α-helix	77	1
β-strand	78-79	2	4
α-helix	80-82	3
α-helix	85-87	3
β-strand	89-93	5	5
β-strand	102-105	4	5
α-helix	106	1
β-strand	109-111	3	6
β-strand	119-121	3	6
α-helix	122-124	3
β-strand	125	1	7
α-helix	126	1
β-strand	129-133	5	8
α-helix	140-141	2
β-strand	142-145	4	8
β-strand	150-151	2	9
β-strand	156	1	7
α-helix	159-161	3
β-strand	162-163	2	9
α-helix	164-165	2
α-helix	168-170	3
β-strand	173-176	4	10
α-helix	183-184	2
β-strand	185-187	3	10

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	13-24	12
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-123	8
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-168	10

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-167	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 5	A, C	protein	177	Homo sapiens	P25942 (AlphaFold model)
Darpin	B, D	protein	159	synthetic construct

Sequence of entity 1 (A, C), FASTA

>7P3I_1 Tumor necrosis factor receptor superfamily member 5 (chains A, C)
EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQH
KYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSD
TICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDRLRLVPR

Sequence of entity 2 (B, D), FASTA

>7P3I_2 Darpin (chains B, D)
GSDLGKKLLQAARAGQLDEVRELLKAGADVNAKDTWGFTPLHIAAESGHLEIVEVLLKAG
ADVNAKDVQGRTPLHIAAHSGHLEIVEVLLKAGADVNAKDFRGWTPLHLAAWSGHLEIVE
ILLKAGADVNAQDKSGKTPADLAARAGHQDIAEVLQKAA

Primary citation

A Multispecific Anti-CD40 DARPin Construct Induces Tumor-Selective CD40 Activation and Tumor Regression. Rigamonti, N., Veitonmaki, N., Domke, C. et al. Cancer Immunol Res (2022) 10:626-640. DOI 10.1158/2326-6066.CIR-21-0553 · PubMed

Other PDB entries of the same protein (UniProt P25942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LB6 1.8 Å, TRAF6-CD40 Complex
1D00 2.0 Å, Structure of tnf receptor associated factor 2 in complex with a 5-residue CD40 peptide
1CZZ 2.7 Å, Structure of tnf receptor associated factor 2 in complex with a 17-residue CD40 peptide
8YX1 2.7 Å, CD40 in complex with Bleselumab Fab
5DMJ 2.79 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB
8YX9 2.8 Å, CD40 in complex with Dacetuzumab Fab
6PE8 2.84 Å, Crystal structure of CD40/ABBV-323 FAB complex
6FAX 2.99 Å, Complex of Human CD40 Ectodomain with Lob 7.4 Fab
6PE9 3.13 Å, Crystal Structure of CD40 complexed to FAB516
5IHL 3.3 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab
1FLL 3.5 Å, Molecular basis for CD40 signaling mediated by TRAF3
3QD6 3.5 Å, Crystal structure of the CD40 and CD154 (CD40L) complex

Browse structure collections

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