7WYB: ADGRL3/Gi complex

ADGRL3/Gi complex. Determined by electron microscopy at 2.97 Å resolution. Released 26 Oct 2022.

Method: Electron microscopy
Resolution: 2.97 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,757
Mol. weight: 284.51 kDa
Released: 26 Oct 2022

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

Secondary structure: helices and β-sheets

7WYB contains 37 α-helices and 62 β-strands across 5 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 B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-29	21
β-strand	34-39	6	1
α-helix	46-53	8
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-211	4
α-helix	213-215	3
β-strand	220-226	7	1
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	1
α-helix	272-278	7
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	329-331	3
α-helix	333-347	15

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-32	3
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-153	8	6
β-strand	156-161	6	6
β-strand	165-169	5	6
β-strand	176-181	6	6
β-strand	187-191	5	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	241-245	5	8
β-strand	250-253	4	8
β-strand	260-264	5	8
β-strand	273-277	5	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	305-308	4	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-42	13
α-helix	45-47	3
α-helix	53-55	3

Chain E: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	15-25	11	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	69-73	5	10
β-strand	78-86	9	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	115-119	5	11
β-strand	142-144	3	12
β-strand	149-150	2	13
β-strand	153	1	14
β-strand	155	1	14
β-strand	157-163	7	12
β-strand	168	1	15
β-strand	174	1	15
β-strand	176-181	6	13
β-strand	188-192	5	13
β-strand	196-197	2	13
β-strand	206-209	4	12
β-strand	213-218	6	12
β-strand	227-233	7	13
α-helix	239	1
β-strand	245-248	4	13

Chain R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	925-928	4
α-helix	941-955	15
α-helix	959-969	11
α-helix	971-973	3
α-helix	976-998	23
α-helix	1008-1037	30
α-helix	1042-1043	2
α-helix	1048-1069	22
β-strand	1074	1	16
β-strand	1082	1	16
α-helix	1089-1091	3
α-helix	1093-1098	6
α-helix	1100-1116	17
α-helix	1144-1153	10
α-helix	1156-1161	6
α-helix	1170-1180	11
α-helix	1183-1188	6
α-helix	1189-1193	5
α-helix	1196-1205	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	247	Homo sapiens
Isoform 3 of Adhesion G protein-coupled receptor L3	R	protein	1543	Mus musculus	Q80TS3 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7WYB_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (C), FASTA

>7WYB_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>7WYB_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>7WYB_4 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 5 (R), FASTA

>7WYB_5 Isoform 3 of Adhesion G protein-coupled receptor L3 (chains R)
MWPPQLLILTMLLAPVVHGGKHNERHPALAAPLRHAERSPGGALPPRHLLQQPAAERSTA
HRGQGPRGAARGVRGPGAPGAQIAAQAFSRAPIPMAVVRRELSCESYPIELRCPGTDVIM
IESANYGRTDDKICDSDPAQMENIRCYLPDAYKIMSQRCNNRTQCAVVAGPDVFPDPCPG
TYKYLEVQYECVPYKVEQKVFLCPGLLKGVYQSEHLFESDHQSGAWCKDPLQASDKIYYM
PWTPYRTDTLTEYSSKDDFIAGRPTTTYKLPHRVDGTGFVVYDGALFFNKERTRNIVKFD
LRTRIKSGEAIIANANYHDTSPYRWGGKSDIDLAVDENGLWVIYATEQNNGKIVISQLNP
YTLRIEGTWDTAYDKRSASNAFMICGILYVVKSVYEDDDNEATGNKIDYIYNTDQSKDSL
VDVPFPNSYQYIAAVDYNPRDNLLYVWNNYHVVKYSLDFGPLDSRSGPVHHGQVSYISPP
IHLDSELERPPVRGISTTGSLGMGSTTTSTTLRTTTWNIGRSTTASLPGRRNRSTSTPSP
AVEVLDDVTTHLPSAASQIPAMEESCEAVEAREIMWFKTRQGQVAKQPCPAGTIGVSTYL
CLAPDGIWDPQGPDLSNCSSPWVNHITQKLKSGETAANIARELAEQTRNHLNAGDITYSV
RAMDQLVGLLDVQLRNLTPGGKDSAARSLNKLQKRERSCRAYVQAMVETVNNLLQPQALN
AWRDLTTSDQLRAATMLLDTVEESAFVLADNLLKTDIVRENTDNIQLEVARLSTEGNLED
LKFPENMGHGSTIQLSANTLKQNGRNGEIRVAFVLYNNLGPYLSTENASMKLGTEAMSTN
HSVIVNSPVITAAINKEFSNKVYLADPVVFTVKHIKQSEENFNPNCSFWSYSKRTMTGYW
STQGCRLLTTNKTHTTCSCNHLTNFAVLMAHVEVKHSDAVHDLLLDVITWVGILLSLVCL
LICIFTFCFFRGLQSDRNTIHKNLCISLFVAELLFLIGINRTDQPIACAVFAALLHFFFL
AAFTWMFLEGVQLYIMLVEVFESEHSRRKYFYLVGYGMPALIVAVSAAVDYRSYGTDKVC
WLRLDTYFIWSFIGPATLIIMLNVIFLGIALYKMFHHTAILKPESGCLDNINYEDNRPFI
KSWVIGAIALLCLLGLTWAFGLMYINESTVIMAYLFTIFNSLQGMFIFIFHCVLQKKVRK
EYGKCLRTHCCSGKSTESSIGSGKTSGSRTPGRYSTGSQSRIRRMWNDTVRKQSESSFIT
GDINSSASLNREPYRETKGLLNNARDTSVMDTLPLNGNHGNSYSIAGGEYLSNCVQIIDR
GYNHNETALEKKILKELTSNYIPSYLNNHERSSEQNRNMMNKLVNNLGSGSEDDAIVLDD
AASFNHEESLGLELIHEESDAPLLPPRVYSTDNHQPHHYSRRRFPQDHSESFFPLLTDEH
TEDLQSPHRDSLYTSMPALAGVPAADSVTTSTQTEAAAAKGGDAEDVYYKSMPNLGSRNH
VHPLHAYYQLGRGSSDGFIVPPNKDGASPEGTSKGPAHLVTSL

Primary citation

Structural insights into adhesion GPCR ADGRL3 activation and G q , G s , G i , and G 12 coupling. Qian, Y., Ma, Z., Liu, C. et al. Mol Cell (2022) 82:4340-4352.e6. DOI 10.1016/j.molcel.2022.10.009 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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