9JKS: 6O-HCAR3-Gi complex

6O-HCAR3-Gi complex. Determined by electron microscopy at 3.31 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.31 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,617
Mol. weight: 145.26 kDa
Ligands: A1EOA
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9JKS contains 37 α-helices and 61 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	24-55	32
α-helix	61-75	15
α-helix	76-78	3
α-helix	80-83	4
α-helix	84-87	4
α-helix	97-129	33
α-helix	135-137	3
α-helix	141-158	18
α-helix	193-217	25
α-helix	224-243	20
α-helix	246-258	13
α-helix	266-283	18
α-helix	286-290	5
α-helix	291-295	5

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	30-33	4
α-helix	38-39	2
β-strand	49-51	3	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-181	7	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	217-223	7	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-307	4	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	212-216	5
β-strand	220-226	7	1
α-helix	227-230	4
α-helix	242-254	13
β-strand	264-269	6	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-298	3
α-helix	304-308	5
β-strand	319-323	5	1
α-helix	331-351	21

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain S: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
α-helix	53-55	3
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	92-94	3	12
β-strand	97-99	3	11
β-strand	107-111	5	11
β-strand	115-117	3	12
β-strand	118-119	2	10
β-strand	141	1	13
β-strand	146-148	3	14
β-strand	155-159	5	15
β-strand	160	1	13
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	14
β-strand	186-190	5	14
β-strand	194-195	2	14
β-strand	203-208	6	15
β-strand	211-216	6	15
β-strand	226-231	6	14
β-strand	239	1	14
β-strand	243-246	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hydroxycarboxylic acid receptor 3	A	protein	301	Homo sapiens	P49019 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	351	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	337	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	56	Homo sapiens	P59768 (AlphaFold model)
ScFv16	S	protein	247	Homo sapiens

Sequence of entity 1 (A), FASTA

>9JKS_1 Hydroxycarboxylic acid receptor 3 (chains A)
MNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQNGTANVCISF
SICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
F

Sequence of entity 2 (C), FASTA

>9JKS_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9JKS_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
LDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHW
GTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSI
YNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGH
TGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFAT
GSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKAD
RAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>9JKS_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 5 (S), FASTA

>9JKS_5 ScFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
A1EOA	3-[bis(thiophen-3-ylmethyl)amino]-1~{H}-pyrazole-5-carboxylic acid	C14 H13 N3 O2 S2	1

Primary citation

Structures of G-protein coupled receptor HCAR3 in complex with selective agonists reveal the basis for ligand recognition and selectivity. Ye, F., Zhang, Z., Zhang, B. et al. PLoS Biol (2025) 23:e3003480-e3003480. DOI 10.1371/journal.pbio.3003480 · PubMed

Other PDB entries of the same protein (UniProt P49019 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JEI 2.73 Å, Cryo-EM Structure of the compuond 5c-HCAR3-Gi complex
9JID 2.78 Å, Cryo-EM Structure of the niacin-HCAR3-Gi complex
8JEF 2.96 Å, Cryo-EM Structure of the 3HO-HCAR3-Gi complex
9KT6 3.01 Å, HCA3-Gi complex with acifran
9JKT 3.05 Å, PLA-HCAR3-Gi complex
8IHJ 3.07 Å, Cryo-EM structure of HCA3-Gi complex with acifran
9JKX 3.18 Å, acifran-HCAR3-Gi complex
8IHK 3.21 Å, Cryo-EM structure of HCA3-Gi complex with acifran (local)
9JKV 3.26 Å, IBC-HCAR3-Gi complex
9JIC 3.4 Å, Cryo-EM Structure of the apo HCAR3-Gi complex

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