8ID9: Eicosapentaenoic acid bound GPR120-Gi complex

Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi complex. Determined by electron microscopy at 3.0 Å resolution. Released 15 Mar 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,996
Mol. weight: 156.76 kDa
Ligands: EPA
Released: 15 Mar 2023

Explore 8ID9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ID9 contains 32 α-helices and 61 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-39	7	14
α-helix	46-52	7
β-strand	185-191	7	14
β-strand	194-200	7	14
α-helix	212-215	4
β-strand	220-225	6	14
α-helix	242-254	13
β-strand	263-268	6	14
α-helix	272-275	4
α-helix	297-308	12
β-strand	319-322	4	14
α-helix	330-351	22

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	38-39	2
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	70-74	5	2
β-strand	78-82	5	2
β-strand	89-94	6	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
α-helix	145	1
β-strand	146-153	8	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	208-212	5	5
β-strand	218-222	5	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	259-264	6	6
α-helix	272	1
β-strand	273-277	5	7
β-strand	285-289	5	7
β-strand	294-297	4	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-70	35
α-helix	79-89	11
α-helix	92-99	8
α-helix	108-139	32
α-helix	152-169	18
α-helix	171-175	5
β-strand	180	1	15
β-strand	193	1	15
α-helix	201-212	12
α-helix	213-217	5
α-helix	218-242	25
α-helix	250-252	3
α-helix	253-275	23
α-helix	278-292	15
α-helix	302-311	10
α-helix	313-321	9

Chain S: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-11	2	9
β-strand	17-25	9	8
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	46-51	6	9
β-strand	58-60	3	9
β-strand	65	1	8
β-strand	68-73	6	8
β-strand	78-84	7	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	111	1	9
β-strand	115-118	4	9
β-strand	141-142	2	10
β-strand	147	1	11
β-strand	156-160	5	12
β-strand	161-162	2	10
β-strand	167	1	13
β-strand	173	1	13
β-strand	175-180	6	11
β-strand	187-191	5	11
β-strand	195-196	2	11
β-strand	204-209	6	12
β-strand	212-217	6	12
β-strand	227-232	6	11
α-helix	238	1
β-strand	244-245	2	11

Chain Y: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-42	13
α-helix	54-55	2
α-helix	56-58	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	Y	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	S	protein	285	Homo sapiens
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Free fatty acid receptor 4	R	protein	361	Homo sapiens	Q5NUL3 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8ID9_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (Y), FASTA

>8ID9_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains Y)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (S), FASTA

>8ID9_3 scFv16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 4 (A), FASTA

>8ID9_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (R), FASTA

>8ID9_5 Free fatty acid receptor 4 (chains R)
MSPECARAAGDAPLRSLEQANRTRFPFFSDVKGDHRLVLAAVETTVLVLIFAVSLLGNVC
ALVLVARRRRRGATACLVLNLFCADLLFISAIPLVLAVRWTEAWLLGPVACHLLFYVMTL
SGSVTILTLAAVSLERMVCIVHLQRGVRGPGRRARAVLLALIWGYSAVAALPLCVFFRVV
PQRLPGADQEISICTLIWPTIPGEISWDVSFVTLNFLVPGLVIVISYSKILQITKASRKR
LTVSLAYSESHQIRVSQQDFRLFRTLFLLMVSFFIMWSPIIITILLILIQNFKQDLVIWP
SLFFWVVAFTFANSALNPILYNMTLCRNEWKKIFCCFWFPEKGAILTDTSVKRNDLSIIS
G

Ligands and cofactors

ID	Name	Formula	Copies
EPA	5,8,11,14,17-eicosapentaenoic acid	C20 H30 O2	1

Primary citation

Unsaturated bond recognition leads to biased signal in a fatty acid receptor. Mao, C., Xiao, P., Tao, X.N. et al. Science (2023) 380:eadd6220-eadd6220. DOI 10.1126/science.add6220 · 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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