7Y24: Octreotide-bound SSTR2-miniGo-scFv16 complex

Cryo-EM structure of the octreotide-bound SSTR2-miniGo-scFv16 complex. Determined by electron microscopy at 3.25 Å resolution. Released 19 Oct 2022.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,229
Mol. weight: 132.41 kDa
Released: 19 Oct 2022

Explore 7Y24 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y24 contains 31 α-helices and 63 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-38	6	1
α-helix	45-52	8
β-strand	186-192	7	1
β-strand	195-201	7	1
α-helix	209-211	3
β-strand	221-226	6	1
α-helix	242-255	14
β-strand	264-269	6	1
α-helix	273-279	7
α-helix	297-309	13
β-strand	319-322	4	1
α-helix	331-351	21

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-40	3
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
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	189-192	4	6
β-strand	198-202	5	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	260-264	5	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	293-298	6	8
β-strand	304-309	6	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	16
β-strand	6-7	2	16

Chain E: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-67	26
α-helix	68-72	5
α-helix	77-104	28
α-helix	112-145	34
α-helix	147-153	7
α-helix	156-179	24
β-strand	182-185	4	17
β-strand	191-194	4	17
α-helix	203-213	11
α-helix	214-218	5
α-helix	220-236	17
α-helix	245-281	37
α-helix	288-309	22
α-helix	310-314	5
α-helix	317-324	8

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	27-29	3
α-helix	30-43	14
α-helix	53-55	3

Chain S: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	19-25	7	9
β-strand	33-39	7	11
β-strand	45-51	7	11
α-helix	53-55	3
β-strand	58-60	3	11
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-117	3	11
β-strand	118-119	2	10
α-helix	125-127	3
β-strand	128-129	2	12
β-strand	134-136	3	13
β-strand	143-147	5	14
β-strand	148-149	2	12
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
β-strand	191-196	6	14
β-strand	199-204	6	14
β-strand	214-219	6	13
α-helix	226-228	3
β-strand	232-234	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(o) subunit alpha	A	protein	224	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	338	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	56	Homo sapiens	P59768 (AlphaFold model)
single Fab chain (svFv16)	S	protein	246	Homo sapiens
Octreotide	C	protein	8	Homo sapiens
Somatostatin receptor type 2	E	protein	327	Homo sapiens	P30874 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7Y24_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
LSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKSTIVKQMKIIHGGSGGSG
GTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIFCVDLSDYNRMHESLMD
FDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQAQFES
KNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 2 (B), FASTA

>7Y24_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>7Y24_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 4 (S), FASTA

>7Y24_4 single Fab chain (svFv16) (chains S)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSS
GGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRP
GQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGA
GTKLEL

Sequence of entity 5 (C), FASTA

>7Y24_5 Octreotide (chains C)
FCFWKTCT

Sequence of entity 6 (E), FASTA

>7Y24_6 Somatostatin receptor type 2 (chains E)
MDMADEPLNGSHTWLSIPFDLNGSVVSTNTSNQTEPYYDLTSNAVLTFIYFVVCIIGLCG
NTLVIYVILRYAKMKTITNIYILNLAIADELFMLGLPFLAMQVALVHWPFGKAICRVVMT
VDGINQFTSIFCLTVMSIDRYLAVVHPIKSAKWRRPRTAKMITMAVWGVSLLVILPIMIY
AGLRSNQWGRSSCTINWPGESGAWYTGFIIYTFILGFLVPLTIICLCYLFIIIKVKSSGI
RVGSSKRKKSEKKVTRMVSIVVAVFIFCWLPFYIFNVSSVSMAISPTPALKGMFDFVVVL
TYANSCANPILYAFLSDNFKKSFQNVL

Primary citation

Molecular basis for the selective G protein signaling of somatostatin receptors. Chen, S., Teng, X., Zheng, S. Nat Chem Biol (2023) 19:133-140. DOI 10.1038/s41589-022-01130-3 · PubMed

Other PDB entries of the same protein (UniProt P09471 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BSB 2.32 Å, Global reconstruction of DRD2 bound to LSD in complex with a mini-GoA and scFv16…
9VJE 2.47 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with buspirone
9K20 2.65 Å, Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGo-scFv16 complex
9VJ5 2.69 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
8E9X 2.7 Å, CryoEM structure of miniGo-coupled hM4Di in complex with DCZ
9T88 2.74 Å, Cryo-EM structure of ESG-2-37-bound D3 dopamine receptor with mini-Go
9VNF 2.74 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with (S)-pindolol
8YN7 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo
8YN8 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with proxyfan and miniGo
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
7W2Z 2.8 Å, Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
8XXH 2.8 Å, Structure of CXCR2 bound to CXCL2 (CXCR2-CXCL2-Go Full map)

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