7WU2: Adhesion GPCR ADGRD1

Cryo-EM structure of the adhesion GPCR ADGRD1 in complex with miniGs. Determined by electron microscopy at 2.8 Å resolution. Released 27 Apr 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 7,829
Mol. weight: 130.7 kDa
Released: 27 Apr 2022

Explore 7WU2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WU2 contains 38 α-helices and 49 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 A: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	27-39	13
β-strand	41-46	6	1
α-helix	54-56	3
β-strand	209-214	6	1
β-strand	217-223	7	1
α-helix	234-238	5
β-strand	243-249	7	1
α-helix	266-277	12
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	308-311	4
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-351	20
β-strand	359-363	5	1
α-helix	371-391	21

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100	1	4
β-strand	104-105	2	5
β-strand	111-113	3	5
β-strand	116	1	4
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-24	16
α-helix	30-43	14
α-helix	45-47	3

Chain N: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-126	5	11

Chain R: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	560-590	31
α-helix	591-593	3
α-helix	602-622	21
α-helix	630-661	32
α-helix	672-676	5
α-helix	677-681	5
α-helix	682-693	12
β-strand	698	1	12
β-strand	706	1	12
α-helix	714-736	23
α-helix	739-744	6
α-helix	746-749	4
α-helix	753-763	11
α-helix	765-769	5
α-helix	771-773	3
α-helix	774-777	4
α-helix	778-780	3
α-helix	784-796	13
α-helix	798-803	6
α-helix	804-808	5
α-helix	811-820	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	243	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Nanobody Nb35	N	protein	162	Lama glama
Adhesion G-protein coupled receptor D1	R	protein	348	Homo sapiens	Q6QNK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7WU2_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGHHHHHHENLYFQGIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHGGSGGS
GGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALN
DFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGED
PRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCRDIIQRMHLRQY
ELL

Sequence of entity 2 (B), FASTA

>7WU2_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7WU2_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>7WU2_4 Nanobody Nb35 (chains N)
MGMKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNW
VRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYC
ARCPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHHEPEA

Sequence of entity 5 (R), FASTA

>7WU2_5 Adhesion G-protein coupled receptor D1 (chains R)
MKTIIALSYIFCLVFAGAPTNFAILMQVVPLELARGHQVALSSISYVGCSLSVLCLVATL
VTFAVLSSVSTIRNQRYHIHANLSFAVLVAQVLLLISFRLEPGTTPCQVMAVLLHYFFLS
AFAWMLVEGLHLYSMVIKVFGSEDSKHRYYYGMGWGFPLLICIISLSFAMDSYGTSNNCW
LSLASGAIWAFVAPALFVIVVNIGILIAVTRVISQISADNYKIHGDPSAFKLTAKAVAVL
LPILGTSWVFGVLAVNGCAVVFQYMFATLNSLQGLFIFLFHCLLNSEVRAAFKHKTKVWS
LTEFLEVLFQGPWSHPQFEKGGGSGGGSGGSAWSHPQFEKDYKDDDDK

Primary citation

Structural basis of tethered agonism of the adhesion GPCRs ADGRD1 and ADGRF1. Qu, X., Qiu, N., Wang, M. et al. Nature (2022) 604:779-785. DOI 10.1038/s41586-022-04580-w · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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