9JCP: PDB entry 9JCP

Cryo-EM structure of the proton-sensing GPCR (GPR4)-Gq protein complex at pH 7.4. Determined by electron microscopy at 2.55 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 2.55 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,331
Mol. weight: 161.87 kDa
Ligands: A1L35, CLR
Released: 9 Jul 2025

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

Secondary structure: helices and β-sheets

9JCP contains 31 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-40	7	12
α-helix	42-44	3
α-helix	46-56	11
β-strand	184-191	8	12
β-strand	194-201	8	12
α-helix	211-215	5
β-strand	220-226	7	12
α-helix	230-245	16
β-strand	253-259	7	12
α-helix	261-270	10
α-helix	275-277	3
α-helix	280-282	3
α-helix	299-317	19
β-strand	326-330	5	12
α-helix	338-357	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-30	20
α-helix	36-39	4
α-helix	43-45	3
β-strand	52-56	5	1
β-strand	63-68	6	2
β-strand	74-79	6	2
β-strand	83-88	6	2
β-strand	94-99	6	2
β-strand	105-110	6	3
β-strand	116-121	6	3
β-strand	125-130	6	3
β-strand	140-145	6	3
β-strand	151-156	6	4
β-strand	161-166	6	4
β-strand	170-175	6	4
β-strand	180-186	7	4
β-strand	194-197	4	5
β-strand	203-207	5	5
β-strand	212-217	6	5
β-strand	222-228	7	5
β-strand	234-239	6	6
β-strand	245-250	6	6
β-strand	255-259	5	6
β-strand	265-269	5	6
β-strand	278-283	6	7
β-strand	289-294	6	7
β-strand	299-303	5	7
β-strand	309-313	5	7
β-strand	322-325	4	1
β-strand	332-335	4	1
β-strand	341-344	4	1

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-22	11
α-helix	30-44	15
α-helix	53-55	3

Chain N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	8
β-strand	11	1	9
β-strand	17-25	9	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	69-73	5	8
β-strand	78-84	7	8
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-124	3	10
β-strand	125	1	9

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-47	29
α-helix	51-78	28
α-helix	87-120	34
α-helix	131-148	18
α-helix	151-154	4
β-strand	161	1	11
β-strand	165	1	11
α-helix	176-184	9
α-helix	185-191	7
α-helix	192-210	19
α-helix	216-253	38
α-helix	261-275	15
α-helix	278-283	6
α-helix	284-288	5
α-helix	291-302	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	R	protein	362	Homo sapiens	P46093 (AlphaFold model)
Guanine nucleotide-binding protein G(q) subunit alpha	A	protein	361	Homo sapiens

Sequence of entity 1 (B), FASTA

>9JCP_1 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 2 (G), FASTA

>9JCP_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 3 (N), FASTA

>9JCP_3 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS

Sequence of entity 4 (R), FASTA

>9JCP_4 G-protein coupled receptor 4 (chains R)
MGNHTWEGCHVDSRVDHLFPPSLYIFVIGVGLPTNCLALWAAYRQVQQRNELGVYLMNLS
IADLLYICTLPLWVDYFLHHDNWIHGPGSCKLFGFIFYTNIYISIAFLCCISVDRYLAVA
HPLRFARLRRVKTAVAVSSVVWATELGANSAPLFHDELFRDRYNHTFCFEKFPMEGWVAW
MNLYRVFVGFLFPWALMLLSYRGILRAVRGSVSTERQEKAKIKRLALSLIAIVLVCFAPY
HVLLLSRSAIYLGRPWDCGFEERVFSAYHSSLAFTSLNCVADPILYCLVNEGARSDVAKA
LHNLLRFLASDKPQEMANASLTLETPLTSKRNSTAKAMTGSWAATPPSQGDQVQLKMLPP
AQ

Sequence of entity 5 (A), FASTA

>9JCP_5 Guanine nucleotide-binding protein G(q) subunit alpha (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNL
V

Ligands and cofactors

ID	Name	Formula	Copies
A1L35	2-[[(2~{R})-3-acetyloxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimet…	C10 H23 N O7 P	2
CLR	Cholesterol	C27 H46 O	1

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

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