8E3Z: VPAC1R-VIP-Gs complex

Cryo-EM structure of the VPAC1R-VIP-Gs complex. Determined by electron microscopy at 2.7 Å resolution. Released 23 Nov 2022.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 8,898
Mol. weight: 163.19 kDa
Released: 23 Nov 2022

Explore 8E3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E3Z contains 39 α-helices and 54 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	17-37	21
β-strand	40-47	8	1
α-helix	53-60	8
β-strand	209-214	6	1
β-strand	217-222	6	1
α-helix	234-238	5
β-strand	243-248	6	1
α-helix	265-277	13
β-strand	286-291	6	1
α-helix	296-299	4
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-349	18
β-strand	359	1	1
β-strand	362	1	1
α-helix	371-390	20

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
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	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
α-helix	145	1
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	168-170	3	5
β-strand	175-178	4	5
β-strand	189-192	4	6
β-strand	198-202	5	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
β-strand	273-276	4	8
β-strand	284	1	9
β-strand	287-289	3	8
β-strand	294-297	4	8
β-strand	298	1	9
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-11	2	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
α-helix	62-64	3
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	122-125	4	11

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-25	24

Chain R: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	40-49	10
α-helix	53-54	2
β-strand	67	1	12
β-strand	72	1	12
β-strand	83-85	3	13
α-helix	86-87	2
α-helix	88-91	4
β-strand	100-102	3	13
β-strand	103	1	14
β-strand	111	1	14
α-helix	129-166	38
α-helix	173-199	27
α-helix	204-209	6
α-helix	213-245	33
α-helix	252-254	3
α-helix	255-279	25
α-helix	294-323	30
α-helix	335-350	16
α-helix	352-356	5
α-helix	365-370	6
α-helix	371-385	15
α-helix	386-390	5
α-helix	393-406	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	394	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Nanobody 35	N	protein	138	Lama glama
Vasoactive intestinal peptide	P	protein	28	Homo sapiens	P01282 (AlphaFold model)
Vasoactive intestinal polypeptide receptor 1	R	protein	462	Homo sapiens	P32241

Sequence of entity 1 (A), FASTA

>8E3Z_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCSVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 2 (B), FASTA

>8E3Z_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8E3Z_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>8E3Z_4 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHHEPEA

Sequence of entity 5 (P), FASTA

>8E3Z_5 Vasoactive intestinal peptide (chains P)
HSDAVFTDNYTRLRKQMAVKKYLNSILN

Sequence of entity 6 (R), FASTA

>8E3Z_6 Vasoactive intestinal polypeptide receptor 1 (chains R)
DYKDDDDLEVLFQGPAARLQEECDYVQMIEVQHKQCLEEAQLENETIGCSKMWDNLTCWP
ATPRGQVVVLACPLIFKLFSSIQGRNVSRSCTDEGWTHLEPGPYPIACGLDDKAASLDEQ
QTMFYGSVKTGYTIGYGLSLATLLVATAILSLFRKLHCTRNYIHMHLFISFILRAAAVFI
KDLALFDSGESDQCSEGSVGCKAAMVFFQYCVMANFFWLLVEGLYLYTLLAVSFFSERKY
FWGYILIGWGVPSTFTMVWTIARIHFEDYGCWDTINSSLWWIIKGPILTSILVNFILFIC
IIRILLQKLRPPDIRKSDSSPYSRLARSTLLLIPLFGVHYIMFAFFPDNFKPEVKMVFEL
VVGSFQGFVVAILYCFLNGEVQAELRRKWRRWHLQGVLGWNPKYRHPSGGSNGATCSTQV
SMLTRVSPGARRSSSFQAEVSLVPAGLEVLFQGPHHHHHHHH

Primary citation

Understanding VPAC receptor family peptide binding and selectivity. Piper, S.J., Deganutti, G., Lu, J. et al. Nat Commun (2022) 13:7013-7013. DOI 10.1038/s41467-022-34629-3 · 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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