9GE2: GPR55

Structure of GPR55 in complex with G13 and synthetic agonist ML184. Determined by electron microscopy at 2.51 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.51 Å
Organisms: Homo sapiens, Mus musculus, Aequorea victoria
Chains: 5
Atoms: 9,081
Mol. weight: 175.97 kDa
Ligands: CLR, A1IKH
Released: 5 Mar 2025

Explore 9GE2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GE2 contains 39 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	7-31	25
β-strand	34-38	5	1
α-helix	46-57	12
β-strand	70-76	7	1
β-strand	79-85	7	1
α-helix	94-98	5
β-strand	105-111	7	1
α-helix	115-117	3
α-helix	118-129	12
α-helix	133-135	3
β-strand	138-144	7	1
α-helix	146-155	10
α-helix	158-160	3
α-helix	172-185	14
β-strand	195-199	5	1
α-helix	207-226	20

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	22-43	22
α-helix	48-51	4
α-helix	56-57	2
β-strand	61	1	2
β-strand	65-69	5	3
β-strand	76-81	6	4
β-strand	87-92	6	4
β-strand	96-101	6	4
β-strand	107-112	6	4
β-strand	118-123	6	5
β-strand	129-134	6	5
β-strand	139-143	5	5
β-strand	152-157	6	5
β-strand	164-169	6	6
β-strand	174-179	6	6
β-strand	183-188	6	6
β-strand	193-199	7	6
β-strand	205-210	6	7
β-strand	216-221	6	7
β-strand	226-230	5	7
β-strand	236-240	5	7
β-strand	247-252	6	8
β-strand	258-263	6	8
β-strand	268-272	5	8
β-strand	277-282	6	8
α-helix	290	1
β-strand	291-296	6	2
β-strand	302-307	6	2
β-strand	312-316	5	2
β-strand	321-326	6	2
β-strand	333-338	6	3
β-strand	345-349	5	3
β-strand	354-357	4	3

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	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	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	114-116	3	11
β-strand	117-118	2	10
α-helix	137-138	2
β-strand	139-140	2	12
β-strand	145-147	3	13
β-strand	154-160	7	12
β-strand	165	1	14
β-strand	171	1	14
β-strand	173-178	6	13
β-strand	185-189	5	13
β-strand	193-194	2	13
α-helix	195	1
β-strand	202-206	5	12
β-strand	210-215	6	12
α-helix	220-222	3
β-strand	224-230	7	13
α-helix	236	1
β-strand	238	1	13
β-strand	242-245	4	13

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain R: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	14-51	38
α-helix	53-83	31
α-helix	93-124	32
α-helix	126-132	7
α-helix	135-157	23
α-helix	179-186	8
α-helix	187-191	5
α-helix	192-209	18
α-helix	210-212	3
α-helix	216-221	6
α-helix	222-253	32
α-helix	262-277	16
α-helix	280-284	5
α-helix	285-289	5
α-helix	293-298	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein subunit…	A	protein	230	Homo sapiens	Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	358	Homo sapiens	P62873 (AlphaFold model)
Single-chain variable fragment ScFv16	F	protein	253	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	80	Homo sapiens	P59768 (AlphaFold model)
Green fluorescent protein,G-protein coupled receptor 55,G-protein coupled receptor 55	R	protein	650	Aequorea victoria, Homo sapiens	Q9Y2T6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GE2_1 Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein subunit alpha-13 (chains A)
MGSTVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 2 (B), FASTA

>9GE2_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (F), FASTA

>9GE2_3 Single-chain variable fragment ScFv16 (chains F)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGGTTLTVSS
GGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRP
GQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGA
GTKLELKLEVLFQ

Sequence of entity 4 (G), FASTA

>9GE2_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSA

Sequence of entity 5 (R), FASTA

>9GE2_5 Green fluorescent protein,G-protein coupled receptor 55,G-protein coupled receptor 55 (chains R)
MKTIIALSYIFCLVFADYKDDDDKKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDAT
YGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTI
SFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQK
NGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHM
VLLEFVTAAGITHGMDELYKAAGSGEFLEVLFQGPGAGSDSMSQQNTSGDCLFDGVNELM
KTLQFAVHIPTFVLGLLLNLLAIHGFSTFLKNRWPDYAATSIYMINLAVFDLLLVLSLPF
KMVLSQVQSPFPSLCTLVECLYFVSMYGSVFTICFISMDRFLAIRYPLLVSHLRSPRKIF
GICCTIWVLVWTGSIPIYSFHGKVEKYMCFHNMSDDTWSAKVFFPLEVFGFLLPMGIMGF
CCSRSIHILLGRRDHTQDWVQQKACIYSIAASLAVFVVSFLPVHLGFFLQFLVRNSFIVE
CRAKQSISFFLQLSMCFSNVNCCLDVFCYYFVIKEFRMNIRAHRPSRVQLVLQDTTISRG
AGSGAGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGAGSHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
A1IKH	3-[4-(2,3-dimethylphenyl)piperazin-1-yl]carbonyl-N,N-dimethyl-4-pyrrolidin-1-yl…	C25 H34 N4 O3 S	1

Primary citation

Structural basis for lipid-mediated activation of G protein-coupled receptor GPR55. Claff, T., Ebenhoch, R., Kley, J.T. et al. Nat Commun (2025) 16:1973-1973. DOI 10.1038/s41467-025-57204-y · PubMed

Other PDB entries of the same protein (UniProt Q14344 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
7SF8 2.7 Å, GPR56 (ADGRG1) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
8ZX4 2.85 Å, LPI-bound GPR55 in complex with G13
9GE3 2.87 Å, Structure of GPR55 in complex with G13 and endogenous lipid agonist…
7SF7 2.9 Å, LPHN3 (ADGRL3) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
9E51 2.9 Å, Cryo-EM structure of human LPHN2 (ADGRL2)/G13 complex in lipid nanodiscs
9ECJ 2.9 Å, Human P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13
9IY8 3.01 Å, Cryo-EM structure of apo-GPR55-G13 complex
8ZX5 3.03 Å, AM251-bound GPR55 in complex with G13
9IZH 3.04 Å, Cryo-EM structure of LPA1-G13 complex with LPA
8KGG 3.06 Å, LPS-bound P2Y10 in complex with G13
7YDH 3.1 Å, Cryo EM structure of CD97/miniG13 complex

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