8ZBE: Octreotide-bound SSTR5-Gi complex

cryo-EM structure of the octreotide-bound SSTR5-Gi complex. Determined by electron microscopy at 3.24 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 3.24 Å
Organisms: Homo sapiens, Oplophorus gracilirostris, Rattus norvegicus
Chains: 6
Atoms: 7,489
Mol. weight: 185.12 kDa
Released: 10 Jul 2024

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

Secondary structure: helices and β-sheets

8ZBE contains 35 α-helices and 65 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: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	43-67	25
α-helix	74-89	16
α-helix	92-101	10
α-helix	110-113	4
α-helix	115-118	4
α-helix	121-141	21
α-helix	144-146	3
α-helix	153-176	24
α-helix	197-206	10
α-helix	207-217	11
α-helix	220-224	5
α-helix	241-260	20
α-helix	262-273	12
α-helix	280-307	28
α-helix	309-315	7

Chain B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	37-39	3	1
α-helix	47-51	5
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	201-203	3
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-224	5	1
α-helix	227-229	3
α-helix	244-255	12
β-strand	263-268	6	1
α-helix	271-280	10
α-helix	296-310	15
β-strand	320-323	4	1
α-helix	333-351	19

Chain C: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	46-51	6	13
β-strand	58-63	6	14
β-strand	69-74	6	14
β-strand	78-83	6	14
β-strand	88-94	7	14
β-strand	100-105	6	15
β-strand	111-116	6	15
β-strand	122-125	4	15
β-strand	134-137	4	15
β-strand	148-153	6	16
β-strand	156-160	5	16
β-strand	165-170	6	16
β-strand	175-176	2	16
β-strand	180-181	2	16
β-strand	187-192	6	17
β-strand	198-203	6	17
β-strand	208-212	5	17
β-strand	222	1	17
β-strand	229-234	6	18
β-strand	240-245	6	18
β-strand	249-254	6	18
β-strand	262-263	2	18
α-helix	271-272	2
β-strand	273-276	4	19
β-strand	284-286	3	20
β-strand	287-289	3	19
β-strand	296-298	3	20
β-strand	303-304	2	20
β-strand	320	1	13
β-strand	327-328	2	13
β-strand	336-340	5	13

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	30-44	15

Chain E: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	12	1	3
β-strand	18-25	8	2
α-helix	29-31	3
β-strand	33	1	4
β-strand	34	1	5
β-strand	36-39	4	6
β-strand	45-47	3	6
β-strand	49-50	2	7
β-strand	51	1	5
β-strand	59-60	2	7
α-helix	62-64	3
β-strand	68-73	6	2
β-strand	78-83	6	2
β-strand	92-94	3	8
β-strand	95-96	2	6
β-strand	97-99	3	4
β-strand	107-111	5	4
β-strand	115-117	3	8
β-strand	119	1	3
β-strand	141	1	9
β-strand	155-157	3	10
β-strand	160	1	9
β-strand	176-179	4	11
β-strand	189-190	2	11
β-strand	194-195	2	11
β-strand	203	1	10
β-strand	206-208	3	12
β-strand	211-213	3	12
β-strand	214-216	3	10
β-strand	226-229	4	11
α-helix	240-242	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein)	A	protein	570	Homo sapiens, Oplophorus gracilirostris	P07550 (AlphaFold model), P35346 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein subunit gamma	D	protein	71	Rattus norvegicus	A0A9X9ZA26 (AlphaFold model)
ScFv16	E	protein	304	Homo sapiens
octreotide	P	protein	8	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	377	Rattus norvegicus	P54311

Sequence of entity 1 (A), FASTA

>8ZBE_1 Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein) (chains A)
MKTIIALSYIFCLVFADYKDDDDKMGQPGNGSAFLLAPNGSHAPDHDVMEPLFPASTPSW
NASSPGAASGGGDNRTLVGPAPSAGARAVLVPVLYLLVCAAGLGGNTLVIYVVLRFAKMK
TVTNIYILNLAVADVLYMLGLPFLATQNAASFWPFGPVLCRLVMTLDGVNQFTSVFCLTV
MSVDRYLAVVHPLSSARWRRPRVAKLASAAAWVLSLCMSLPLLVFADVQEGGTCNASWPE
PVGLWGAVFIIYTAVLGFFAPLLVICLCYLLIVVKVRAAGVRVGCVRRRSERKVTRMVLV
VVLVFAGCWLPFFTVNIVNLAVALPQEPASAGLYFFVVILSYANSCANPVLYGFLSDNFR
QSFQKVLCLRKGSGAKDADATEPRPDRIRQQQEATPPAHRAAANGLMQTSKLVFTLEDFV
GDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSA
DQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITV
TGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 2 (B), FASTA

>8ZBE_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (D), FASTA

>8ZBE_3 Guanine nucleotide-binding protein subunit gamma (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>8ZBE_4 ScFv16 (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELVDENLYFQGASHHHH
HHHH

Sequence of entity 5 (P), FASTA

>8ZBE_5 octreotide (chains P)
FCFWKTCT

Sequence of entity 6 (C), FASTA

>8ZBE_6 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Primary citation

Structural insights into somatostatin receptor 5 bound with cyclic peptides. Li, Y.G., Meng, X.Y., Yang, X. et al. Acta Pharmacol Sin (2024) 45:2432-2440. DOI 10.1038/s41401-024-01314-8 · PubMed

Other PDB entries of the same protein (UniProt P07550 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GQ4 1.9 Å, Structural determinants of the nherf interaction with BETA2AR and pdgfr
2RH1 2.4 Å, High resolution crystal structure of human B2-adrenergic G protein-coupled receptor.
6PS2 2.4 Å, XFEL beta2 AR structure by ligand exchange from Timolol to Alprenolol.
9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
9RKF 2.45 Å, Dark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at…
9RKG 2.45 Å, Mixed model refinement of beta-2 Adrenergic receptor with photoazolol in dark state and…
5D5A 2.48 Å, In meso in situ serial X-ray crystallography structure of the Beta2-adrenergic receptor…
6PS3 2.5 Å, XFEL beta2 AR structure by ligand exchange from Timolol to Carvedilol.
9Q3L 2.5 Å, CryoEM structure of beta2-adrenergic receptor dimer mediated by a biased allosteric…
9RKH 2.5 Å, Dark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at…
9WG0 2.59 Å, D1R-Gs in complexed with SKF81297/LY3154207/BMSA1/UNC10062
6PS4 2.6 Å, XFEL beta2 AR structure by ligand exchange from Timolol to ICI-118551.

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