8X8N: PDB entry 8X8N

Cryo-EM structure of the octreotide-bound Somatostatin receptor 5-Gi protein complex. Determined by electron microscopy at 2.9 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,769
Mol. weight: 156.22 kDa
Released: 12 Jun 2024

Explore 8X8N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X8N contains 35 α-helices and 56 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	7-19	13
α-helix	22-30	9
β-strand	34-39	6	1
α-helix	46-54	9
β-strand	184-191	8	1
β-strand	194-201	8	1
α-helix	211-215	5
β-strand	220-226	7	1
α-helix	234-244	11
β-strand	253-259	7	1
α-helix	261-269	9
α-helix	288-289	2
α-helix	300-302	3
α-helix	305-317	13
β-strand	326-330	5	1
α-helix	339-358	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	37-39	3
β-strand	52-56	5	2
β-strand	63-68	6	3
β-strand	74-79	6	3
β-strand	83-88	6	3
β-strand	93-99	7	3
β-strand	105-110	6	4
β-strand	116-121	6	4
β-strand	126-130	5	4
β-strand	139-140	2	4
β-strand	151-155	5	5
β-strand	161-166	6	5
β-strand	170-175	6	5
β-strand	180-186	7	5
β-strand	192-197	6	6
β-strand	203-208	6	6
β-strand	213-217	5	6
β-strand	226-227	2	6
β-strand	234-239	6	7
β-strand	245-250	6	7
β-strand	255-259	5	7
β-strand	268-269	2	7
β-strand	278-283	6	8
β-strand	289-294	6	8
β-strand	299-303	5	8
β-strand	309-312	4	8
β-strand	320-325	6	2
β-strand	332-336	5	2
β-strand	341-344	4	2

Chain E: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	69-73	5	9
β-strand	78-84	7	9
β-strand	93-99	7	11
β-strand	111	1	11
β-strand	116	1	11
β-strand	117-119	3	10
β-strand	138-139	2	12
β-strand	155-161	7	12
β-strand	175-179	5	13
β-strand	186-190	5	13
β-strand	194-195	2	13
β-strand	204-207	4	12
β-strand	211-216	6	12
α-helix	221-223	3
β-strand	226-230	5	13
β-strand	239	1	13
β-strand	243	1	13

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-21	13
α-helix	29-42	14
α-helix	55-57	3

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	44-67	24
α-helix	75-89	15
α-helix	93-100	8
α-helix	109-123	15
α-helix	125-142	18
α-helix	149-151	3
α-helix	153-171	19
α-helix	173-176	4
α-helix	182-184	3
α-helix	194-206	13
α-helix	207-211	5
α-helix	212-234	23
α-helix	242-259	18
α-helix	263-273	11
α-helix	280-291	12
α-helix	292-295	4
α-helix	296-306	11
α-helix	309-314	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha	A	protein	360	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	371	Homo sapiens	P62873 (AlphaFold model)
ScFv16	E	protein	248	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	70	Homo sapiens	P59768 (AlphaFold model)
Somatostatin receptor type 5	R	protein	364	Homo sapiens	P35346 (AlphaFold model)
octreotide	C	protein	8	Homo sapiens

Sequence of entity 1 (A), FASTA

>8X8N_1 Guanine nucleotide-binding protein G(i) subunit alpha (chains A)
GCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
SGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFK
SIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRV
TRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDVTDIIIKMNLRDCGLF

Sequence of entity 2 (B), FASTA

>8X8N_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSG
VSGWRLFKKIS

Sequence of entity 3 (E), FASTA

>8X8N_3 ScFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 4 (G), FASTA

>8X8N_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 5 (R), FASTA

>8X8N_5 Somatostatin receptor type 5 (chains R)
MEPLFPASTPSWNASSPGAASGGGDNRTLVGPAPSAGARAVLVPVLYLLVCAAGLGGNTL
VIYVVLRFAKMKTVTNIYILNLAVADVLYMLGLPFLATQNAASFWPFGPVLCRLVMTLDG
VNQFTSVFCLTVMSVDRYLAVVHPLSSARWRRPRVAKLASAAAWVLSLCMSLPLLVFADV
QEGGTCNASWPEPVGLWGAVFIIYTAVLGFFAPLLVICLCYLLIVVKVRAAGVRVGCVRR
RSERKVTRMVLVLVLVFAGCWLPFFTVNIVNLAVALPQEPASAGLYFFVVILSYANSCAN
PVLYGFLSDNFRQSFQKVLCLRKGSGAKDADATEPRPDRIRQQQEATPPAHRAAANGLMQ
TSKL

Sequence of entity 6 (C), FASTA

>8X8N_6 octreotide (chains C)
FCFWKTCT

Primary citation

Structural basis for activation of somatostatin receptor 5 by cyclic neuropeptide agonists. Li, J., You, C., Li, Y. et al. Proc Natl Acad Sci U S A (2024) 121:e2321710121-e2321710121. DOI 10.1073/pnas.2321710121 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
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

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