8DJG: ADGRL3-lectin domain

ADGRL3-lectin domain in complex with an activating synthetic antibody fragment. Determined by X-ray diffraction at 2.65 Å resolution. Released 15 Feb 2023.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: synthetic construct, Homo sapiens
Chains: 6
Atoms: 8,099
Mol. weight: 121.72 kDa
Released: 15 Feb 2023

Explore 8DJG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DJG contains 36 α-helices and 102 β-strands across 6 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: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	13-15	3	2
β-strand	20-28	9	1
α-helix	32-34	3
β-strand	35-42	8	2
β-strand	48-55	8	2
β-strand	60-63	4	2
β-strand	68	1	1
β-strand	71-76	6	1
α-helix	77-79	3
β-strand	81-87	7	1
α-helix	91-93	3
β-strand	95-103	9	2
β-strand	115	1	2
β-strand	119-123	5	2
β-strand	129	1	3
α-helix	130-131	2
β-strand	132-136	5	4
β-strand	148-157	10	4
β-strand	158	1	3
β-strand	163-166	4	5
α-helix	167-169	3
β-strand	175-177	3	4
α-helix	178-180	3
β-strand	181-182	2	4
β-strand	188-196	9	4
β-strand	207-212	6	5
β-strand	217-222	6	5

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
β-strand	10-14	5	6
β-strand	20-23	4	7
β-strand	34-39	6	6
β-strand	46-50	5	6
β-strand	54-55	2	6
α-helix	56	1
β-strand	63-68	6	7
β-strand	71-76	6	7
α-helix	81-83	3
β-strand	86-92	7	6
β-strand	97-99	3	6
β-strand	103-107	5	6
β-strand	112	1	8
α-helix	113-114	2
β-strand	115-119	5	9
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	9
β-strand	141	1	8
β-strand	146-151	6	10
β-strand	154-157	4	10
β-strand	160-164	5	9
α-helix	165-168	4
β-strand	174-183	10	9
α-helix	184-187	4
β-strand	192-198	7	10
β-strand	206-211	6	10

Chain C: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	11
β-strand	14-15	2	12
β-strand	21-28	8	11
α-helix	32-34	3
β-strand	37-42	6	13
β-strand	48-55	8	13
β-strand	60-63	4	13
β-strand	71-76	6	11
β-strand	81-86	6	11
α-helix	91-93	3
β-strand	95-100	6	13
β-strand	115	1	13
β-strand	116	1	11
β-strand	119-121	3	13
β-strand	122-123	2	12
α-helix	126-128	3
β-strand	129	1	14
α-helix	130-131	2
β-strand	132-136	5	15
β-strand	147-157	11	15
β-strand	158	1	14
β-strand	163-166	4	16
α-helix	167-169	3
β-strand	171	1	16
β-strand	175-177	3	15
α-helix	178-180	3
β-strand	181-182	2	15
β-strand	188-197	10	15
α-helix	198-200	3
β-strand	207	1	17
β-strand	208-212	5	16
α-helix	213-215	3
β-strand	217-219	3	16
β-strand	222	1	17

Chain D: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
β-strand	10-14	5	18
β-strand	19-23	5	10
β-strand	34-39	6	18
β-strand	46-50	5	18
β-strand	54-55	2	18
α-helix	56	1
β-strand	63-68	6	10
β-strand	71-76	6	10
α-helix	81-83	3
β-strand	86-92	7	18
β-strand	97-99	3	18
α-helix	100-102	3
β-strand	103-107	5	18
α-helix	108	1
β-strand	112	1	19
α-helix	113-114	2
β-strand	115-119	5	20
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	20
β-strand	141	1	19
β-strand	145-151	7	7
β-strand	155-157	3	7
β-strand	160-164	5	20
α-helix	165-168	4
β-strand	174-183	10	20
α-helix	184-187	4
β-strand	192-199	8	7
β-strand	206-211	6	7

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	31-36	6	21
β-strand	40-44	5	22
β-strand	50-59	10	21
β-strand	60	1	23
α-helix	70-73	4
β-strand	78	1	23
α-helix	83-91	9
β-strand	96-100	5	22
β-strand	116-124	9	21

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	30-36	7	24
β-strand	40-44	5	25
β-strand	50-59	10	24
β-strand	60	1	26
α-helix	70-73	4
β-strand	78	1	26
α-helix	82-91	10
β-strand	96-100	5	25
β-strand	116-124	9	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
sAB Heavy Chain	A, C	protein	233	synthetic construct
sAB Light Chain	B, D	protein	215	synthetic construct
Isoform 2 of Adhesion G protein-coupled receptor L3	E, F	protein	109	Homo sapiens	Q9HAR2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8DJG_1 sAB Heavy Chain (chains A, C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNIYYSSIHWVRQAPGKGLEWVAYISPYSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYKYGQGHMGAFDYWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (B, D), FASTA

>8DJG_2 sAB Light Chain (chains B, D)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSNTELVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, F), FASTA

>8DJG_3 Isoform 2 of Adhesion G protein-coupled receptor L3 (chains E, F)
PIPMAVVRRELSCESYPIELRCPGTDVIMIESANYGRTDDKICDSDPAQMENIRCYLPDA
YKIMSQRCNNRTQCAVVAGPDVFPDPCPGTYKYLEVQYECVPYHHHHHH

Primary citation

Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder. Kordon, S.P., Dutka, P., Adamska, J.M. et al. Nat Commun (2023) 14:635-635. DOI 10.1038/s41467-023-36312-7 · PubMed

Other PDB entries of the same protein (UniProt Q9HAR2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFB 2.16 Å, Crystal structure of the Latrophilin3 Lectin and Olfactomedin Domains
7SF7 2.9 Å, LPHN3 (ADGRL3) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
6VHH 2.97 Å, Human Teneurin-2 and human Latrophilin-3 binary complex
8JMT 3.36 Å, Structure of the adhesion GPCR ADGRL3 in the apo state
5CMN 3.6 Å, FLRT3 LRR domain in complex with LPHN3 Olfactomedin domain
8VTI 3.9 Å, Latrophilin-3 (ADGRL3) HormR and GAIN domains in the context of the holoreceptor

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