9JCQ: PDB entry 9JCQ

Cryo-EM structure of the proton-sensing GPCR (GPR4)-Gs protein complex at pH 7.4. Determined by electron microscopy at 2.59 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 2.59 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,431
Mol. weight: 162.41 kDa
Ligands: CLR, A1L35
Released: 9 Jul 2025

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

Secondary structure: helices and β-sheets

9JCQ contains 38 α-helices and 47 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	1
α-helix	46-51	6
β-strand	184-191	8	1
β-strand	194-201	8	1
α-helix	211-215	5
β-strand	220-226	7	1
α-helix	233-245	13
α-helix	247-249	3
β-strand	253-259	7	1
α-helix	261-270	10
α-helix	275-278	4
α-helix	280-282	3
α-helix	293-294	2
α-helix	299-319	21
β-strand	326-330	5	1
α-helix	338-357	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-30	20
α-helix	35-38	4
β-strand	51-56	6	2
β-strand	63-68	6	3
β-strand	74-79	6	3
β-strand	83-88	6	3
β-strand	94-99	6	3
β-strand	105-110	6	4
β-strand	116-121	6	4
β-strand	125-130	6	4
β-strand	139-145	7	4
β-strand	151-158	8	5
β-strand	161-166	6	5
β-strand	171-175	5	5
β-strand	180-185	6	5
β-strand	192-197	6	6
β-strand	203-208	6	6
β-strand	212-217	6	6
β-strand	223-227	5	6
β-strand	234-239	6	7
β-strand	245-250	6	7
β-strand	255-259	5	7
β-strand	264-269	6	7
β-strand	278-282	5	8
β-strand	289-294	6	8
β-strand	299-303	5	8
β-strand	308-313	6	8
β-strand	320-325	6	2
β-strand	332-336	5	2
β-strand	341-345	5	2

Chain D: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-47	29
α-helix	51-67	17
α-helix	70-78	9
α-helix	87-90	4
α-helix	95-120	26
α-helix	127-129	3
α-helix	137-148	12
α-helix	151-154	4
β-strand	160	1	11
β-strand	166	1	11
α-helix	176-184	9
α-helix	185-191	7
α-helix	192-209	18
α-helix	216-253	38
α-helix	259-262	4
α-helix	265-274	10
α-helix	275-277	3
α-helix	278-283	6
α-helix	284-288	5
α-helix	291-305	15

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-21	12
α-helix	30-34	5
α-helix	37-43	7
α-helix	53-55	3

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-11	2	10
β-strand	18-25	8	9
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
α-helix	109-111	3
β-strand	118	1	10
β-strand	122-125	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha	A	protein	361	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	518	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)
Nanobody 35	N	protein	128	Lama glama
G-protein coupled receptor 4	D	protein	362	Homo sapiens	P46093 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JCQ_1 Guanine nucleotide-binding protein G(s) subunit alpha (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L

Sequence of entity 2 (B), FASTA

>9JCQ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSG
VFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVI
IPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAV
FDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 3 (G), FASTA

>9JCQ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 4 (N), FASTA

>9JCQ_4 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS

Sequence of entity 5 (D), FASTA

>9JCQ_5 G-protein coupled receptor 4 (chains D)
MGNHTWEGCHVDSRVDHLFPPSLYIFVIGVGLPTNCLALWAAYRQVQQRNELGVYLMNLS
IADLLYICTLPLWVDYFLHHDNWIHGPGSCKLFGFIFYTNIYISIAFLCCISVDRYLAVA
HPLRFARLRRVKTAVAVSSVVWATELGANSAPLFHDELFRDRYNHTFCFEKFPMEGWVAW
MNLYRVFVGFLFPWALMLLSYRGILRAVRGSVSTERQEKAKIKRLALSLIAIVLVCFAPY
HVLLLSRSAIYLGRPWDCGFEERVFSAYHSSLAFTSLNCVADPILYCLVNEGARSDVAKA
LHNLLRFLASDKPQEMANASLTLETPLTSKRNSTAKAMTGSWAATPPSQGDQVQLKMLPP
AQ

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
A1L35	2-[[(2~{R})-3-acetyloxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimet…	C10 H23 N O7 P	2

Primary citation

Molecular mechanism of pH sensing and activation in GPR4 reveals proton-mediated GPCR signaling. You, C., Guo, S., Zhang, T. et al. Cell Discov (2025) 11:59-59. DOI 10.1038/s41421-025-00807-y · 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

Browse structure collections

About this viewer

MolViewer shows 9JCQ 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.