9JFX: GPR4

Cryo-EM structure of GPR4 complexed with miniGs/q in pH7.5. Determined by electron microscopy at 2.87 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 2.87 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,154
Mol. weight: 136.25 kDa
Released: 23 Apr 2025

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

Secondary structure: helices and β-sheets

9JFX contains 32 α-helices and 48 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	11-37	27
β-strand	40-46	7	1
α-helix	53-59	7
β-strand	207-214	8	1
β-strand	217-224	8	1
α-helix	235-237	3
β-strand	243-249	7	1
α-helix	256-267	12
β-strand	276-282	7	1
α-helix	284-292	9
α-helix	298-301	4
α-helix	322-337	16
β-strand	349-353	5	1
α-helix	362-380	19

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	43	1	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	91-94	4	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	217-223	7	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	2
β-strand	284-289	6	2
β-strand	294-298	5	2
β-strand	303-308	6	2
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-22	16
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-11	2	10
β-strand	19-25	7	9
β-strand	34-39	6	10
β-strand	46-51	6	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	69-73	5	9
β-strand	78-82	5	9
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-125	4	10

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	20-47	28
α-helix	51-68	18
α-helix	70-78	9
α-helix	87-119	33
α-helix	127-129	3
α-helix	131-149	19
α-helix	151-154	4
β-strand	158	1	11
β-strand	168	1	11
α-helix	176-187	12
α-helix	191-209	19
α-helix	218-252	35
α-helix	259-262	4
α-helix	265-274	10
α-helix	278-283	6
α-helix	284-288	5
α-helix	291-303	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	262	Homo sapiens	P63092 (AlphaFold model)
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	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Nanobody 35	N	protein	157	Lama glama
G-protein coupled receptor 4	R	protein	374	Homo sapiens	P46093 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JFX_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MHHHHHHENLYFQGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGADNS
GKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVT
AIIFVVDSSDYNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYF
PEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENA
RRIFNDCKDIILQMNLREYNLV

Sequence of entity 2 (B), FASTA

>9JFX_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 (C), FASTA

>9JFX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>9JFX_4 Nanobody 35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAMQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWV
RQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCA
RCPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Sequence of entity 5 (R), FASTA

>9JFX_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 P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
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
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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