8ZX5: AM251-bound GPR55

AM251-bound GPR55 in complex with G13. Determined by electron microscopy at 3.03 Å resolution. Released 13 Nov 2024.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,106
Mol. weight: 109.57 kDa
Ligands: A1D9D
Released: 13 Nov 2024

Explore 8ZX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZX5 contains 30 α-helices and 37 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-27	19
β-strand	34-39	6	1
α-helix	42-44	3
α-helix	46-52	7
β-strand	70-76	7	1
β-strand	79-85	7	1
α-helix	89-91	3
α-helix	95-97	3
β-strand	105-111	7	1
α-helix	115-129	15
α-helix	132-134	3
β-strand	138-144	7	1
α-helix	147-150	4
α-helix	158-160	3
α-helix	172-184	13
β-strand	195-196	2	1
β-strand	199	1	1
α-helix	207-227	21

Chain B: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
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	121-125	5	4
β-strand	134-139	6	4
α-helix	145	1
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	217-223	7	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-264	6	7
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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	35-44	10
α-helix	45-47	3

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-50	35
α-helix	60-75	16
α-helix	78-81	4
β-strand	88	1	9
α-helix	91-124	34
α-helix	128-131	4
α-helix	135-152	18
α-helix	155-157	3
β-strand	166	1	9
α-helix	174-176	3
α-helix	179-186	8
α-helix	187-191	5
α-helix	192-209	18
α-helix	216-219	4
α-helix	223-239	17
α-helix	241-253	13
α-helix	260-277	18
α-helix	280-283	4

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	319	Homo sapiens	Q9Y2T6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8ZX5_1 engineered miniGalpha 13 (chains A)
MGSTVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 2 (B), FASTA

>8ZX5_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

>8ZX5_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8ZX5_4 G-protein coupled receptor 55 (chains R)
MSQQNTSGDCLFDGVNELMKTLQFAVHIPTFVLGLLLNLLAIHGFSTFLKNRWPDYAATS
IYMINLAVFDLLLVLSLPFKMVLSQVQSPFPSLCTLVECLYFVSMYGSVFTICFISMDRF
LAIRYPLLVSHLRSPRKIFGICCTIWVLVWTGSIPIYSFHGKVEKYMCFHNMSDDTWSAK
VFFPLEVFGFLLPMGIMGFCCSRSIHILLGRRDHTQDWVQQKACIYSIAASLAVFVVSFL
PVHLGFFLQFLVRNSFIVECRAKQSISFFLQLSMCFSNVNCCLDVFVYYFVIKEFRMNIR
AHRPSRVQLVLQDTTISRG

Ligands and cofactors

ID	Name	Formula	Copies
A1D9D	1-(2,4-dichlorophenyl)-5-(4-iodophenyl)-4-methyl-~{N}-piperidin-1-yl-pyrazole-3…	C22 H21 Cl2 I N4 O	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
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
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

About this viewer

MolViewer shows 8ZX5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.