9GE3: GPR55

Structure of GPR55 in complex with G13 and endogenous lipid agonist lysophosphatidylinositol. Determined by electron microscopy at 2.87 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.87 Å
Organisms: Homo sapiens, Mus musculus, Aequorea victoria
Chains: 5
Atoms: 8,563
Mol. weight: 175.49 kDa
Ligands: A1IKT, NAG
Released: 5 Mar 2025

Explore 9GE3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GE3 contains 36 α-helices and 60 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	27-32	6
β-strand	34-38	5	1
α-helix	46-52	7
β-strand	70-76	7	1
β-strand	79-85	7	1
α-helix	94-97	4
α-helix	98-100	3
β-strand	105-111	7	1
α-helix	118-129	12
α-helix	132-134	3
β-strand	138-144	7	1
α-helix	147-155	9
α-helix	172-184	13
β-strand	195	1	1
β-strand	199	1	1
α-helix	207-226	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	48-52	5
α-helix	56-57	2
β-strand	65-70	6	2
β-strand	76-81	6	3
β-strand	87-92	6	3
β-strand	96-101	6	3
β-strand	106-112	7	3
β-strand	118-123	6	4
β-strand	129-134	6	4
β-strand	138-143	6	4
β-strand	152-158	7	4
β-strand	164-171	8	5
β-strand	174-179	6	5
β-strand	183-187	5	5
β-strand	194-199	6	5
β-strand	205-210	6	6
β-strand	216-221	6	6
β-strand	226-230	5	6
β-strand	236-240	5	6
β-strand	247-252	6	7
β-strand	258-263	6	7
β-strand	267-272	6	7
β-strand	277-283	7	7
β-strand	291-296	6	8
β-strand	302-307	6	8
β-strand	311-316	6	8
β-strand	321-327	7	8
β-strand	333-338	6	2
β-strand	345-349	5	2
β-strand	353-357	5	2

Chain F: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	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	1	10
β-strand	95-99	5	11
β-strand	116-118	3	10
β-strand	139-140	2	12
β-strand	145	1	13
β-strand	154-158	5	14
β-strand	159-160	2	12
β-strand	165	1	15
β-strand	171	1	15
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	14
β-strand	211-215	5	14
β-strand	224-230	7	13
α-helix	236	1
β-strand	238	1	13
β-strand	242-244	3	13

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	31-43	13
α-helix	45-47	3

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	13-46	34
α-helix	48-51	4
α-helix	53-82	30
α-helix	93-124	32
α-helix	126-131	6
α-helix	135-157	23
α-helix	179-186	8
α-helix	187-191	5
α-helix	192-209	18
α-helix	211-214	4
α-helix	216-221	6
α-helix	224-234	11
α-helix	236-251	16
α-helix	263-276	14
α-helix	277-279	3
α-helix	280-284	5
α-helix	285-289	5
α-helix	293-299	7

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

>9GE3_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

>9GE3_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

>9GE3_3 Single-chain variable fragment ScFv16 (chains F)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGGTTLTVSS
GGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRP
GQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGA
GTKLELKLEVLFQ

Sequence of entity 4 (G), FASTA

>9GE3_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSA

Sequence of entity 5 (R), FASTA

>9GE3_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
A1IKT	[(2R)-2-oxidanyl-3-[oxidanyl-[(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohe…	C25 H49 O12 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	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
9GE2 2.51 Å, Structure of GPR55 in complex with G13 and synthetic agonist ML184
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
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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