9JKT: PLA-HCAR3-Gi complex

PLA-HCAR3-Gi complex. Determined by electron microscopy at 3.05 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,466
Mol. weight: 154.48 kDa
Ligands: HF2
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9JKT contains 34 α-helices and 59 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, 0 β-strands

Element	Residues	Length
α-helix	25-50	26
α-helix	51-55	5
α-helix	61-78	18
α-helix	80-88	9
α-helix	97-130	34
α-helix	135-138	4
α-helix	141-159	19
α-helix	161-164	4
α-helix	188-217	30
α-helix	224-260	37
α-helix	270-294	25

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	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	166-170	5	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	199-203	5	6
β-strand	207-210	4	6
β-strand	220-223	4	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	303-307	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-38	5	1
α-helix	46-52	7
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	228-231	4
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
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, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	12	1	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	93-99	7	11
β-strand	111	1	11
β-strand	115	1	11
β-strand	119	1	10
β-strand	141	1	12
β-strand	146-148	3	13
β-strand	155-160	6	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
β-strand	203-208	6	12
β-strand	211-216	6	12
β-strand	226-231	6	13
β-strand	239	1	13
β-strand	243-246	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hydroxycarboxylic acid receptor 3	A	protein	387	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

>9JKT_1 Hydroxycarboxylic acid receptor 3 (chains A)
MNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQNGTANVCISF
SICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKITGEPDNNRSTSVELTGDPNKTRGAPEALIANSGEPWSPSYLGP
TSNNHSKKGHCHQEPASLEKQLGCCIE

Sequence of entity 2 (C), FASTA

>9JKT_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9JKT_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

>9JKT_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 5 (S), FASTA

>9JKT_5 ScFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
HF2	(2R)-2-hydroxy-3-phenylpropanoic acid	C9 H10 O3	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
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
9JKS 3.31 Å, 6O-HCAR3-Gi complex
9JIC 3.4 Å, Cryo-EM Structure of the apo HCAR3-Gi complex

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