8ZX4: LPI-bound GPR55

LPI-bound GPR55 in complex with G13. Determined by electron microscopy at 2.85 Å resolution. Released 13 Nov 2024.

Method: Electron microscopy
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,753
Mol. weight: 107.09 kDa
Ligands: A1D9E
Released: 13 Nov 2024

Explore 8ZX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZX4 contains 35 α-helices and 34 β-strands across 4 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-25	17
α-helix	27-30	4
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	70-76	7	1
β-strand	79-85	7	1
α-helix	89-91	3
β-strand	105-111	7	1
α-helix	115-117	3
α-helix	118-129	12
α-helix	132-134	3
β-strand	138-144	7	1
α-helix	147-153	7
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, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-25	17
α-helix	30-33	4
α-helix	34-36	3
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	89-94	6	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	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	189-192	4	6
β-strand	198-202	5	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	1
β-strand	273-278	6	8
β-strand	284-289	6	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 G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	15-23	9
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain R: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	13-50	38
α-helix	57-83	27
α-helix	91-124	34
α-helix	126-131	6
α-helix	135-151	17
α-helix	154-157	4
α-helix	179-186	8
α-helix	187-191	5
α-helix	192-209	18
α-helix	210-213	4
α-helix	218-221	4
α-helix	222-253	32
α-helix	260-276	17
α-helix	277-279	3
α-helix	280-287	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
engineered miniGalpha 13	A	protein	230	Homo sapiens	Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
G-protein coupled receptor 55	R	protein	297	Homo sapiens	Q9Y2T6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8ZX4_1 engineered miniGalpha 13 (chains A)
MGSTVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 2 (B), FASTA

>8ZX4_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8ZX4_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8ZX4_4 G-protein coupled receptor 55 (chains R)
MSQQNTSGDCLFDGVNELMKTLQFAVHIPTFVLGLLLNLLAIHGFSTFLKNRWPDYAATS
IYMINLAVFDLLLVLSLPFKMVLSQVQSPFPSLCTLVECLYFVSMYGSVFTICFISMDRF
LAIRYPLLVSHLRSPRKIFGICCTIWVLVWTGSIPIYSFHGKVEKYMCFHNMSDDTWSAK
VFFPLEVFGFLLPMGIMGFCCSRSIHILLGRRDHTQDWVQQKACIYSIAASLAVFVVSFL
PVHLGFFLQFLVRNSFIVECRAKQSISFFLQLSMCFSNVNCCLDVFVYYFVIKEFRM

Ligands and cofactors

ID	Name	Formula	Copies
A1D9E	[(2~{R})-2-oxidanyl-3-[oxidanyl-[(2~{S},3~{R},5~{R},6~{R})-2,3,4,5,6-pentakis(o…	C25 H49 O12 P	1

Primary citation

Structural insight into GPR55 ligand recognition and G-protein coupling. Xia, R., Yuan, Q., Wang, N. et al. Cell Res (2025) 35:76-79. DOI 10.1038/s41422-024-01044-w · 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
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

Browse structure collections

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