9IY8: Apo-GPR55-G13 complex

Cryo-EM structure of apo-GPR55-G13 complex. Determined by electron microscopy at 3.01 Å resolution. Released 1 Jan 2025.

Method: Electron microscopy
Resolution: 3.01 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,014
Mol. weight: 135.66 kDa
Released: 1 Jan 2025

Explore 9IY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IY8 contains 37 α-helices and 57 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	22-47	26
β-strand	49-55	7	15
α-helix	61-70	10
β-strand	207-213	7	15
β-strand	216-222	7	15
α-helix	231-235	5
β-strand	242-248	7	15
α-helix	252-264	3
α-helix	265-276	12
β-strand	285-291	7	15
α-helix	293-300	8
α-helix	305-308	4
α-helix	319-333	15
β-strand	342-345	4	15
α-helix	354-373	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-151	6	4
β-strand	157-161	5	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	189-192	4	5
β-strand	198-202	5	5
β-strand	208-212	5	5
β-strand	218-222	5	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	249-254	6	6
β-strand	259-265	7	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	335-339	5	1

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	13-50	38
α-helix	58-85	28
α-helix	91-124	34
α-helix	126-131	6
α-helix	135-163	29
α-helix	179-186	8
α-helix	187-191	5
α-helix	192-210	19
α-helix	211-213	3
α-helix	217-221	5
α-helix	222-253	32
α-helix	257-259	3
α-helix	260-278	19
α-helix	280-284	5
α-helix	285-289	5
α-helix	293-301	9

Chain S: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
α-helix	12-13	2
β-strand	17-25	9	8
β-strand	33-39	7	9
β-strand	45-51	7	9
α-helix	53-55	3
β-strand	58-60	3	9
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-84	7	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	111	1	9
β-strand	115-117	3	9
β-strand	141-142	2	10
β-strand	149-150	2	11
β-strand	156-160	5	12
β-strand	161-162	2	10
β-strand	167	1	13
β-strand	173	1	13
β-strand	175-180	6	14
β-strand	187-191	5	14
β-strand	195-196	2	14
α-helix	197	1
β-strand	204-208	5	12
β-strand	213-217	5	12
β-strand	227-232	6	14
β-strand	247-248	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	346	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	70	Homo sapiens	P59768 (AlphaFold model)
G-protein coupled receptor 55	R	protein	318	Homo sapiens	Q9Y2T6 (AlphaFold model)
scFV16	S	protein	251	Homo sapiens
Guanine nucleotide-binding protein subunit alpha-13	A	protein	230	Homo sapiens	Q14344 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9IY8_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
IGRARGFSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGH
LAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVAC
GGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETG
QQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICF
FPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNC
NVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (G), FASTA

>9IY8_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 3 (R), FASTA

>9IY8_3 G-protein coupled receptor 55 (chains R)
SQQNTSGDCLFDGVNELMKTLQFAVHIPTFVLGLLLNLLAIHGFSTFLKNRWPDYAATSI
YMINLAVFDLLLVLSLPFKMVLSQVQSPFPSLCTLVECLYFVSMYGSVFTRCFISMDRFL
AIRYPLLVSHLRSPRKIFGICCTIWVLVWTGSIPIYSFHGKVEKYMCFHNMSDDTWSAKV
FFPLEVFGFLLPMGIMGFCCSRSIHILLGRRDHTQDWVQQKACIYSIAASLAVFVVSFLP
VHLGFFLQFLVRNSFIVECRAKQSISFFLQLSMCFSNVNCCLDVFCYYFVIKEFRMNIRA
HRPSRVQLVLQDTTISRG

Sequence of entity 4 (S), FASTA

>9IY8_4 scFV16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 5 (A), FASTA

>9IY8_5 Guanine nucleotide-binding protein subunit alpha-13 (chains A)
MGSTLSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Primary citation

Structure basis of ligand recognition and activation of GPR55. Chang, H., Li, X., Shen, L. et al. Cell Res (2025) 35:80-83. DOI 10.1038/s41422-024-01046-8 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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