7SGM: CD40 ligand

Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with blocked excited state proton transfer and in complex with its antigen, CD40L. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Feb 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 9
Atoms: 14,354
Mol. weight: 193.89 kDa
Ligands: NAG, TMO
Released: 2 Feb 2022

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

Secondary structure: helices and β-sheets

7SGM contains 59 α-helices and 176 β-strands across 9 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, B and C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	1
β-strand	137	1	2
β-strand	139-141	3	1
β-strand	147-148	2	1
β-strand	153-156	4	2
β-strand	160-163	4	2
β-strand	167-179	13	1
β-strand	189-196	8	2
β-strand	203-210	8	2
α-helix	211-213	3
β-strand	219-231	13	1
β-strand	236-241	6	2
α-helix	244-246	3
β-strand	247	1	1
β-strand	255-260	6	1

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-52	8	8
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
β-strand	107-108	2	8
β-strand	112-116	5	8
β-strand	122	1	9
α-helix	123-124	2
β-strand	125-129	5	10
β-strand	140-150	11	10
β-strand	151	1	9
β-strand	156-159	4	11
α-helix	160-162	3
β-strand	164	1	11
β-strand	168-170	3	10
α-helix	171-173	3
β-strand	174-175	2	10
β-strand	181-190	10	10
α-helix	193-196	4
β-strand	200-205	6	11
β-strand	210-215	6	11

Chain K: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
α-helix	7-9	3
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	33-39	7	19
β-strand	46-51	6	19
β-strand	58-60	3	19
α-helix	62-64	3
β-strand	68-73	6	18
α-helix	74-76	3
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	107-108	2	19
β-strand	112-116	5	19
β-strand	122	1	20
α-helix	123-124	2
β-strand	125-129	5	21
β-strand	140-150	11	21
β-strand	151	1	20
β-strand	156-159	4	22
α-helix	160-162	3
β-strand	164	1	22
β-strand	168-170	3	21
α-helix	171-173	3
β-strand	174-175	2	21
β-strand	181-190	10	21
α-helix	191-193	3
β-strand	194	1	23
β-strand	197	1	23
β-strand	199-205	7	22
α-helix	206-208	3
β-strand	210-216	7	22

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	30	1	14
β-strand	35	1	14
β-strand	37-42	6	13
β-strand	49-53	5	13
β-strand	57-58	2	13
α-helix	59	1
β-strand	66-71	6	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	88-94	7	13
α-helix	100	1
β-strand	102	1	13
β-strand	106-110	5	13
β-strand	115	1	15
α-helix	116-117	2
β-strand	118-122	5	16
α-helix	123-125	3
β-strand	136-143	8	16
β-strand	144	1	15
β-strand	149-154	6	17
β-strand	157-158	2	17
α-helix	159	1
β-strand	163-167	5	16
α-helix	168-171	4
β-strand	177-183	7	16
β-strand	195-201	7	17
β-strand	209-214	6	17

Chain M: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	30	1	26
β-strand	35	1	26
β-strand	37-42	6	25
β-strand	49-53	5	25
β-strand	57-58	2	25
α-helix	59	1
β-strand	66-71	6	24
β-strand	74-79	6	24
α-helix	84-86	3
β-strand	89-94	6	25
α-helix	100	1
β-strand	102	1	25
β-strand	106-110	5	25
β-strand	115	1	27
α-helix	116-117	2
β-strand	118-122	5	28
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	28
β-strand	144	1	27
β-strand	149-154	6	29
β-strand	157-158	2	29
α-helix	159	1
β-strand	163-167	5	28
α-helix	168-171	4
β-strand	177-186	10	28
α-helix	187-191	5
β-strand	195-201	7	29
β-strand	209-214	6	29

Chain X: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	30
α-helix	7-9	3
β-strand	10-12	3	31
β-strand	18-25	8	30
α-helix	29-31	3
β-strand	33-39	7	31
β-strand	46-51	6	31
β-strand	58-60	3	31
α-helix	62-64	3
β-strand	68-73	6	30
α-helix	74-76	3
β-strand	78-83	6	30
α-helix	88-90	3
β-strand	92-99	8	31
β-strand	107-108	2	31
β-strand	112-116	5	31
β-strand	122	1	32
α-helix	123-124	2
β-strand	125-129	5	33
β-strand	140-150	11	33
β-strand	151	1	32
β-strand	156-159	4	34
α-helix	160-162	3
β-strand	164	1	34
β-strand	168-170	3	33
α-helix	171-173	3
β-strand	174-175	2	33
β-strand	181-190	10	33
α-helix	191-193	3
β-strand	200-205	6	34
α-helix	206-208	3
β-strand	210-215	6	34

Chain Y: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-13	4	36
β-strand	19-25	7	35
β-strand	30	1	37
β-strand	35	1	37
β-strand	37-42	6	36
β-strand	49-53	5	36
β-strand	57-58	2	36
α-helix	59	1
β-strand	66-71	6	35
β-strand	74-79	6	35
α-helix	84-86	3
β-strand	88-94	7	36
α-helix	100	1
β-strand	102	1	36
β-strand	106-110	5	36
β-strand	115	1	38
α-helix	116-117	2
β-strand	118-122	5	39
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	39
β-strand	144	1	38
β-strand	149-154	6	40
β-strand	157-158	2	40
α-helix	159	1
β-strand	163-167	5	39
α-helix	168-171	4
β-strand	177-186	10	39
α-helix	187-191	5
β-strand	195-201	7	40
β-strand	209-214	6	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD40 ligand	A, B, C	protein	146	Homo sapiens	P29965 (AlphaFold model)
5c8* Fab heavy chain	H, K, X	protein	226	Homo sapiens
5c8* Fab light chain	L, M, Y	protein	218	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>7SGM_1 CD40 ligand (chains A, B, C)
GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQV
TFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGA
SVFVNVTDPSQVSHGTGFTSFGLLKL

Sequence of entity 2 (H, K, X), FASTA

>7SGM_2 5c8* Fab heavy chain (chains H, K, X)
QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLELIGEINPSNGDTNF
NEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L, M, Y), FASTA

>7SGM_3 5c8* Fab light chain (chains L, M, Y)
DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLES
GVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEXPPTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
TMO	trimethylamine oxide	C3 H9 N O	3

Water and common crystallization additives (TRS, PEG) are not listed.

Primary citation

Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment. Henderson, J.N., Simmons, C.R., Mills, J.H. J Mol Biol (2022) 434:167455-167455. DOI 10.1016/j.jmb.2022.167455 · 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
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
9I5N 3.4 Å, Single particle cryo electron microscopy of a Fab fragment bound to recombinant human…
3QD6 3.5 Å, Crystal structure of the CD40 and CD154 (CD40L) complex

Browse structure collections

About this viewer

MolViewer shows 7SGM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.