9JFZ: Intermediate state GPR4

Cryo-EM structure of intermediate state GPR4 complexed with miniGs/q in pH7.5. Determined by electron microscopy at 2.9 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,198
Mol. weight: 136.25 kDa
Released: 23 Apr 2025

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

Secondary structure: helices and β-sheets

9JFZ contains 30 α-helices and 49 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	10-37	28
β-strand	41-46	6	1
α-helix	53-62	10
β-strand	208-214	7	1
β-strand	217-223	7	1
α-helix	234-237	4
β-strand	243-249	7	1
α-helix	256-267	12
β-strand	276-282	7	1
α-helix	284-293	10
α-helix	298-301	4
α-helix	322-337	16
β-strand	349-353	5	1
α-helix	361-380	20

Chain B: 4 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	229-232	4	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	260-264	5	8
α-helix	272	1
β-strand	273-277	5	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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-22	16
α-helix	30-43	14

Chain N: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	10-11	2	10
β-strand	17	1	11
β-strand	20-25	6	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	84	1	11
β-strand	92-98	7	10
β-strand	122-125	4	10

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-47	29
α-helix	51-75	25
α-helix	87-89	3
α-helix	90-94	5
α-helix	95-119	25
α-helix	131-149	19
α-helix	158-162	5
β-strand	163	1	12
β-strand	169	1	12
α-helix	178-187	10
α-helix	191-209	19
α-helix	216-253	38
α-helix	259-263	5
α-helix	266-274	9
α-helix	278-283	6
α-helix	284-288	5
α-helix	291-299	9

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

>9JFZ_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MHHHHHHENLYFQGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGADNS
GKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVT
AIIFVVDSSDYNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYF
PEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENA
RRIFNDCKDIILQMNLREYNLV

Sequence of entity 2 (B), FASTA

>9JFZ_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

>9JFZ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>9JFZ_4 Nanobody 35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAMQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWV
RQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCA
RCPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Sequence of entity 5 (R), FASTA

>9JFZ_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)

Browse structure collections

About this viewer

MolViewer shows 9JFZ 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.