8VTI: PDB entry 8VTI

Latrophilin-3 (ADGRL3) HormR and GAIN domains in the context of the holoreceptor. Determined by electron microscopy at 3.9 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,667
Mol. weight: 126.84 kDa
Ligands: NAG
Released: 11 Dec 2024

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

Secondary structure: helices and β-sheets

8VTI contains 15 α-helices and 52 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.

Chain A: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	501-502	2	1
β-strand	506-507	2	1
β-strand	518-520	3	2
α-helix	521-522	2
β-strand	523	1	3
β-strand	525	1	3
β-strand	528-530	3	2
β-strand	535	1	4
β-strand	539	1	4
α-helix	554-564	11
α-helix	568-578	11
α-helix	585-608	24
α-helix	619-645	27
α-helix	648-650	3
α-helix	651-656	6
α-helix	659-682	24
β-strand	689-690	2	5
β-strand	693	1	5
β-strand	697-704	8	5
β-strand	714-715	2	6
β-strand	725-726	2	6
α-helix	729-734	6
β-strand	741-748	8	5
α-helix	752-754	3
β-strand	775-776	2	7
β-strand	781-786	6	5
α-helix	794	1
β-strand	795-805	11	6
α-helix	806	1
β-strand	817-824	8	5
β-strand	829-833	5	5
β-strand	837-842	6	6
β-strand	846-853	8	6

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	856-860	5	5
β-strand	861-862	2	7

Chain C: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	11-12	2	9
β-strand	20-22	3	10
β-strand	25	1	11
β-strand	26	1	8
β-strand	34-35	2	12
β-strand	36-39	4	9
β-strand	45-50	6	9
β-strand	54-55	2	9
α-helix	56	1
β-strand	63-67	5	10
β-strand	71	1	11
β-strand	72-76	5	10
β-strand	86-87	2	9
β-strand	90-91	2	12
β-strand	103-105	3	9

Chain D: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	13
β-strand	13-14	2	14
β-strand	20-28	9	13
β-strand	35	1	15
β-strand	37-42	6	14
β-strand	48-54	7	14
β-strand	61	1	14
α-helix	65-67	3
β-strand	71-76	6	13
α-helix	77-79	3
β-strand	81-87	7	13
β-strand	95-100	6	14
β-strand	101	1	16
β-strand	103	1	15
β-strand	116	1	16
β-strand	121-124	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 4 of Adhesion G protein-coupled receptor L3	A	protein	375	Homo sapiens	Q9HAR2 (AlphaFold model)
Isoform 4 of Adhesion G protein-coupled receptor L3	B	protein	314	Homo sapiens	Q9HAR2 (AlphaFold model)
sAB Light Chain	C	protein	215	synthetic construct
sAB Heavy Chain	D	protein	235	synthetic construct

Sequence of entity 1 (A), FASTA

>8VTI_1 Isoform 4 of Adhesion G protein-coupled receptor L3 (chains A)
DYKDDDDAMAQIPALEESCEAVEAREIMWFKTRQGQIAKQPCPAGTIGVSTYLCLAPDGI
WDPQGPDLSNCSSPWVNHITQKLKSGETAANIARELAEQTRNHLNAGDITYSVRAMDQLV
GLLDVQLRNLTPGGKDSAARSLNKLQKRERSCRAYVQAMVETVNNLLQPQALNAWRDLTT
SDQLRAATMLLHTVEESAFVLADNLLKTDIVRENTDNIKLEVARLSTEGNLEDLKFPENM
GHGSTIQLSANTLKQNGRNGEIRVAFVLYNNLGPYLSTENASMKLGTEALSTNHSVIVNS
PVITAAINKEFSNKVYLADPVVFTVKHIKQSEENFNPNCSFWSYSKRTMTGYWSTQGCRL
LTTNKTHTTCSCNHL

Sequence of entity 2 (B), FASTA

>8VTI_2 Isoform 4 of Adhesion G protein-coupled receptor L3 (chains B)
TNFAVLMAHVEVKHSDAVHDLLLDVITWVGILLSLVCLLICIFTFCFFRGLQSDRNTIHK
NLCISLFVAELLFLIGINRTDQPIACAVFAALLHFFFLAAFTWMFLEGVQLYIMLVEVFE
SEHSRRKYFYLVGYGMPALIVAVSAAVDYRSYGTDKVCWLRLDTYFIWSFIGPATLIIML
NVIFLGIALYKMFHHTAILKPESGCLDNINYEDNRPFIKSWVIGAIALLCLLGLTWAFGL
MYINESTVIMAYLFTIFNSLQGMFIFIFHCVLQKKVRKEYGKCLRTHCCSGKSTESSIGS
GKTSGSHHHHHHHH

Sequence of entity 3 (C), FASTA

>8VTI_3 sAB Light Chain (chains C)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSGQYPLTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D), FASTA

>8VTI_4 sAB Heavy Chain (chains D)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSYIHWVRQAPGKGLEWVASISPYSGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHNYWQWWEYSYALDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Conformational coupling between extracellular and transmembrane domains modulates holo-adhesion GPCR function. Kordon, S.P., Cechova, K., Bandekar, S.J. et al. Nat Commun (2024) 15:10545-10545. DOI 10.1038/s41467-024-54836-4 · 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
8DJG 2.65 Å, ADGRL3-lectin domain in complex with an activating synthetic antibody fragment
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

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