9JHP: GPR4

Cryo-EM structure of GPR4 complexed with miniG13 in pH6.8. Determined by electron microscopy at 3.35 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.35 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,683
Mol. weight: 145.84 kDa
Released: 23 Apr 2025

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

Secondary structure: helices and β-sheets

9JHP contains 32 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	34-40	7	1
α-helix	46-54	9
β-strand	69-75	7	1
β-strand	80-86	7	1
α-helix	95-97	3
β-strand	105-110	6	1
α-helix	115-129	15
β-strand	138-143	6	1
α-helix	149-152	4
α-helix	158-160	3
α-helix	172-186	15
β-strand	195-199	5	1
α-helix	207-224	18
α-helix	225-229	5

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	38-39	2
β-strand	49-51	3	2
β-strand	58-62	5	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	91-94	4	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	208-212	5	6
β-strand	221-222	2	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
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	307	1	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain C: 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: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-47	29
α-helix	52-78	27
α-helix	87-97	11
α-helix	100-119	20
α-helix	131-148	18
α-helix	151-154	4
β-strand	158-160	3	16
β-strand	166-168	3	16
α-helix	178-186	9
α-helix	187-191	5
α-helix	192-209	18
α-helix	216-253	38
α-helix	259-275	17
α-helix	278-283	6
α-helix	284-288	5
α-helix	291-295	5

Chain S: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	17-25	9	9
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	78-84	7	9
α-helix	88-90	3
β-strand	93-99	7	11
β-strand	110-111	2	11
β-strand	115	1	11
β-strand	118-119	2	10
β-strand	141-142	2	12
β-strand	156-160	5	13
β-strand	161-162	2	12
β-strand	167-168	2	14
β-strand	172-173	2	14
β-strand	175-180	6	15
β-strand	187-191	5	15
β-strand	195-196	2	15
β-strand	204-209	6	13
β-strand	212-217	6	13
β-strand	227-232	6	15
α-helix	238	1
β-strand	245	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein subunit alpha-13	A	protein	230	Homo sapiens	Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	346	Homo sapiens	P62873 (AlphaFold model)
scFv16	S	protein	286	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
G-protein coupled receptor 4	R	protein	374	Homo sapiens	P46093 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JHP_1 Guanine nucleotide-binding protein subunit alpha-13 (chains A)
MGSTVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 2 (B), FASTA

>9JHP_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
IGRARGFSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGH
LAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVAC
GGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETG
QQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICF
FPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNC
NVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (S), FASTA

>9JHP_3 scFv16 (chains S)
MVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQA
PEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSI
YYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCR
SSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLE
AEDVGVYYCMQHLEYPLTFGAGTKLELKAAAENLYFQSHHHHHHHH

Sequence of entity 4 (C), FASTA

>9JHP_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>9JHP_5 G-protein coupled receptor 4 (chains R)
MGNHTWEGCHVDSRVDHLFPPSLYIFVIGVGLPTNCLALWAAYRQVQQRNELGVYLMNLS
IADLLYICTLPLWVDYFLHHDNWIHGPGSCKLFGFIFYTNIYISIAFLCCISVDRYLAVA
HPLRFARLRRVKTAVAVSSVVWATELGANSAPLFHDELFRDRYNHTFCFEKFPMEGWVAW
MNLYRVFVGFLFPWALMLLSYRGILRAVRGSVSTERQEKAKIKRLALSLIAIVLVCFAPY
HVLLLSRSAIYLGRPWDCGFEERVFSAYHSSLAFTSLNCVADPILYCLVNEGARSDVAKA
LHNLLRFLASDKPQEMANASLTLETPLTSKRNSTAKAMTGSWAATPPSQGDQVQEFLEVL
FQGPHHHHHHHHHH

Primary citation

Structural basis of stepwise proton sensing-mediated GPCR activation. Yue, X., Peng, L., Liu, S. et al. Cell Res (2025) 35:423-436. DOI 10.1038/s41422-025-01092-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
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

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