5DMI: Extracellular domain of the CD40

Structure of the extracellular domain of the CD40 in complex with CHI220 FAB. Determined by X-ray diffraction at 3.69 Å resolution. Released 1 Jun 2016.

Method: X-ray diffraction
Resolution: 3.69 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 4,012
Mol. weight: 67.55 kDa
Released: 1 Jun 2016

Explore 5DMI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DMI contains 13 α-helices and 60 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: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	1
β-strand	37	1	1
β-strand	41	1	2
β-strand	45-46	2	3
β-strand	52	1	4
β-strand	55	1	4
β-strand	60-61	2	3
β-strand	66-67	2	5
β-strand	72	1	2
β-strand	78-79	2	5
α-helix	85-87	3
β-strand	89	1	6
β-strand	93	1	7
β-strand	102	1	7
β-strand	105	1	6
β-strand	110-111	2	8
β-strand	119-120	2	8

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	7-9	3
β-strand	10-12	3	10
β-strand	18-25	8	9
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	57-59	3	10
β-strand	67-72	6	9
α-helix	73-75	3
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-94	7	10
β-strand	102-103	2	10
β-strand	107-111	5	10
α-helix	115-116	2
β-strand	117	1	11
β-strand	120-124	5	12
β-strand	137-147	11	12
β-strand	148	1	11
β-strand	153-157	4	13
β-strand	166	1	13
β-strand	171-173	3	12
α-helix	174-176	3
β-strand	177-178	2	12
β-strand	185-194	10	12
α-helix	199-203	4
β-strand	208-212	5	13
α-helix	213-215	3
β-strand	217-221	5	13

Chain L: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	14
β-strand	10-13	4	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
β-strand	62-67	6	14
β-strand	70-75	6	14
β-strand	84-90	7	15
β-strand	97	1	10
β-strand	99	1	14
β-strand	103-106	4	15
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	144-150	7	18
β-strand	153-155	3	18
β-strand	159-163	5	17
α-helix	165-167	3
β-strand	173-182	10	17
α-helix	183-188	6
β-strand	191-198	8	18
β-strand	205-210	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 5	A	protein	183	Homo sapiens	P25942 (AlphaFold model)
Chi220 Fab heavy chain	H	protein	223	Mus musculus, Homo sapiens
Chi220 Fab light chain	L	protein	213	Mus musculus, Homo sapiens

Sequence of entity 1 (A), FASTA

>5DMI_1 Tumor necrosis factor receptor superfamily member 5 (chains A)
PTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKY
CDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTI
CEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGPQDRLRDPGGGGGRL
VPR

Sequence of entity 2 (H), FASTA

>5DMI_2 Chi220 Fab heavy chain (chains H)
QIQLVQSGPELKKPGETVRISCKASGYAFTTTGMQWVQEMPGKGLKWIGWINTHSGVPKY
VEDFKGRFAFSLETSANTAYLQISNLKNEDTATYFCVRSGNGNYDLAYFAYWGQGTLVTV
SAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (L), FASTA

>5DMI_3 Chi220 Fab light chain (chains L)
DIVLTQSPATLSVTPGDRVSLSCRASQSISDYLHWYQQKSHESPRLLIKYASHSISGIPS
RFSGSGSGSDFTLSINSVEPEDVGIYYCQHGHSFPWTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Primary citation

Functional Antagonism of Human CD40 Achieved by Targeting a Unique Species-Specific Epitope. Yamniuk, A.P., Suri, A., Krystek, S.R. et al. J Mol Biol (2016) 428:2860-2879. DOI 10.1016/j.jmb.2016.05.014 · 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
7P3I 2.29 Å, Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein
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

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