8ZCJ: Pasireotide-bound SSTR5-Gi complex

Cryo-EM structure of the pasireotide-bound SSTR5-Gi complex. Determined by electron microscopy at 3.09 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 3.09 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 6
Atoms: 7,808
Mol. weight: 184.98 kDa
Released: 10 Jul 2024

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

Secondary structure: helices and β-sheets

8ZCJ contains 35 α-helices and 63 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	33-38	6	1
α-helix	46-52	7
β-strand	185-187	3	1
β-strand	195-200	6	1
α-helix	213-215	3
β-strand	220-225	6	1
α-helix	244-254	11
β-strand	263-268	6	1
α-helix	271-280	10
α-helix	296-299	4
α-helix	300-304	5
α-helix	305-309	5
β-strand	319-323	5	1
α-helix	330-348	19

Chain C: 2 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
β-strand	46-51	6	2
β-strand	52	1	3
β-strand	54	1	3
β-strand	58-62	5	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-103	4	5
β-strand	111	1	6
β-strand	114-116	3	5
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	148-149	2	7
β-strand	156-160	5	7
β-strand	166-170	5	7
β-strand	176-180	5	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	221-223	3	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	260-264	5	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-317	3	11
β-strand	320	1	2
β-strand	327-329	3	2
β-strand	330-331	2	11
β-strand	336-340	5	2

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	35-43	9

Chain E: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	12
β-strand	78-83	6	12
β-strand	92-94	3	15
β-strand	95-99	5	14
α-helix	110	1
β-strand	111	1	14
α-helix	112	1
β-strand	115-117	3	15
β-strand	118-119	2	13
β-strand	155-158	4	16
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-179	6	18
β-strand	185-187	3	18
β-strand	189-190	2	19
β-strand	194-195	2	19
β-strand	203-208	6	16
β-strand	211-216	6	16
β-strand	226-231	6	18
β-strand	244	1	18

Chain G: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	44-62	19
α-helix	63-67	5
α-helix	74-91	18
α-helix	93-97	5
α-helix	111-115	5
α-helix	116-137	22
α-helix	138-142	5
α-helix	147-150	4
α-helix	153-171	19
α-helix	194-206	13
α-helix	207-211	5
α-helix	213-218	6
α-helix	219-227	9
α-helix	228-232	5
α-helix	244-261	18
α-helix	263-273	11
α-helix	275-277	3
α-helix	280-303	24
α-helix	309-315	7

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	377	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Bos taurus	P63212 (AlphaFold model)
ScFv16	E	protein	304	Homo sapiens
Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein)	G	protein	570	Homo sapiens, Oplophorus gracilirostris	P07550 (AlphaFold model), P35346
004-dtr-lys-tyr-pha-hyp	A	protein	6	synthetic construct

Sequence of entity 1 (B), FASTA

>8ZCJ_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (C), FASTA

>8ZCJ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Sequence of entity 3 (D), FASTA

>8ZCJ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>8ZCJ_4 ScFv16 (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELVDENLYFQGASHHHH
HHHH

Sequence of entity 5 (G), FASTA

>8ZCJ_5 Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein) (chains G)
MKTIIALSYIFCLVFADYKDDDDKMGQPGNGSAFLLAPNGSHAPDHDVMEPLFPASTPSW
NASSPGAASGGGDNRTLVGPAPSAGARAVLVPVLYLLVCAAGLGGNTLVIYVVLRFAKMK
TVTNIYILNLAVADVLYMLGLPFLATQNAASFWPFGPVLCRLVMTLDGVNQFTSVFCLTV
MSVDRYLAVVHPLSSARWRRPRVAKLASAAAWVLSLCMSLPLLVFADVQEGGTCNASWPE
PVGLWGAVFIIYTAVLGFFAPLLVICLCYLLIVVKVRAAGVRVGCVRRRSERKVTRMVLV
VVLVFAGCWLPFFTVNIVNLAVALPQEPASAGLYFFVVILSYANSCANPVLYGFLSDNFR
QSFQKVLCLRKGSGAKDADATEPRPDRIRQQQEATPPAHRAAANGLMQTSKLVFTLEDFV
GDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSA
DQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITV
TGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 6 (A), FASTA

>8ZCJ_6 004-DTR-LYS-TYR-PHA-HYP (chains A)
XWKYFP

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 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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