9EGO: PDB entry 9EGO

Cannabinoid receptor 1-Gi complex with novel ligand. Determined by electron microscopy at 3.2 Å resolution. Released 30 Apr 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,469
Mol. weight: 169.85 kDa
Ligands: YVF
Released: 30 Apr 2025

Explore 9EGO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EGO contains 37 α-helices and 59 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	14-23	10
β-strand	34-38	5	1
α-helix	45-52	8
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-230	4
α-helix	241-254	14
β-strand	263-269	7	1
α-helix	274-277	4
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-34	5
α-helix	38-39	2
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	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	157-161	5	5
β-strand	165-169	5	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	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
α-helix	272-273	2
β-strand	275-278	4	8
β-strand	284-288	5	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	53-55	3

Chain R: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	129-132	4
α-helix	137-139	3
α-helix	154-160	7
α-helix	162-165	4
α-helix	169-177	9
α-helix	190-193	4
α-helix	205-213	9
α-helix	230-232	3
α-helix	236-238	3
α-helix	276-283	8
α-helix	297-310	14
α-helix	348-350	3
α-helix	359-367	9
α-helix	379-382	4
α-helix	383-385	3
α-helix	393-396	4
α-helix	403-406	4

Chain S: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-12	3	10
β-strand	19-24	6	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	69-73	5	9
β-strand	78-82	5	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	111	1	10
β-strand	115-119	5	10
β-strand	128-129	2	11
β-strand	135-136	2	12
β-strand	143-149	7	11
β-strand	154	1	13
β-strand	160	1	13
β-strand	162-167	6	14
β-strand	174-179	6	14
β-strand	182-183	2	14
β-strand	191-196	6	11
β-strand	199-204	6	11
β-strand	214-219	6	14
β-strand	227	1	14
α-helix	230	1
β-strand	231-232	2	14
β-strand	233-234	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	344	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Cannabinoid receptor 1	R	protein	495	Homo sapiens	P21554 (AlphaFold model)
scFv16	S	protein	259	Mus musculus

Sequence of entity 1 (A), FASTA

>9EGO_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9EGO_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
PGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>9EGO_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>9EGO_4 Cannabinoid receptor 1 (chains R)
DYKDDDDAMKSILDGLADTTFRTITTDLLYVGSNDIQYEDIKGDMASKLGYFPQKFPLTS
FRGSPFQEKMTAGDNPQLVPADQVNITEFYNKSLSENLYFQGSFKENEENIQCGENFMDI
ECFMVLNPSQQLAIAVLSLTLGTFTVLENLLVLCVILHSRSLRCRPSYHFIGSLAVADLL
GSVIFVYSFIDFHVFHRKDSRNVFLFKLGGVTASFTASVGSLFLTAIDRYISIHRPLAYK
RIVTRPKAVVAFCLMWTIAIVIAVLPLLGWNCEKLQSVCSDIFPHIDETYLMFWIGVTSV
LLLFIVYAYMYILWKAHSHAVRMIQRGTQKSIIIHTSEDGKVQVTRPDQARMDIRLAKTL
VLILVVLIICWGPLLAIMVYDVFGKMNKLIKTVFAFCSMLCLLNSTVNPIIYALRSKDLR
HAFRSMFPSCEGTAQPLDNSMGDSDCLHKHANNAASVHRAAESCIKSTVKIAKVTMSVST
DTSAEALGSHHHHHH

Sequence of entity 5 (S), FASTA

>9EGO_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
YVF	methyl (2R)-2-({(1M)-5-methyl-1-[3-(trifluoromethyl)phenyl]-1H-pyrazole-3-carbo…	C20 H18 F3 N3 O3 S	1

Primary citation

Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects. Tummino, T.A., Iliopoulos-Tsoutsouvas, C., Braz, J.M. et al. Nat Commun (2025) 16:2237-2237. DOI 10.1038/s41467-025-57136-7 · 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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