9JKV: IBC-HCAR3-Gi complex

IBC-HCAR3-Gi complex. Determined by electron microscopy at 3.26 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,922
Mol. weight: 154.52 kDa
Ligands: A1EB5
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9JKV contains 34 α-helices and 63 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	25-49	25
α-helix	50-52	3
α-helix	61-82	22
α-helix	99-130	32
α-helix	135-138	4
α-helix	141-163	23
α-helix	189-212	24
α-helix	213-218	6
α-helix	224-259	36
α-helix	266-289	24
α-helix	290-292	3
α-helix	293-296	4

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-49	3	2
β-strand	52	1	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	135-140	6	5
β-strand	146-151	6	6
β-strand	157-161	5	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	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	293-298	6	9
β-strand	304-309	6	9
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335	1	3
β-strand	338-339	2	2

Chain C: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185	1	1
β-strand	188-190	3	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	227-230	4
α-helix	242-254	13
α-helix	257-259	3
β-strand	264-269	6	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	302-308	7
β-strand	319-324	6	1
α-helix	330-350	21

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-44	15
α-helix	45-47	3
α-helix	54-55	2

Chain S: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	10
β-strand	10-12	3	11
β-strand	17-23	7	10
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
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-84	7	10
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
β-strand	141	1	12
β-strand	146-148	3	13
β-strand	153-159	7	14
β-strand	160	1	12
β-strand	166	1	15
β-strand	172	1	15
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
α-helix	196	1
β-strand	203-204	2	14
β-strand	207-208	2	14
β-strand	211-219	9	14
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

>9JKV_1 Hydroxycarboxylic acid receptor 3 (chains A)
MNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQNGTANVCISF
SICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKITGEPDNNRSTSVELTGDPNKTRGAPEALIANSGEPWSPSYLGP
TSNNHSKKGHCHQEPASLEKQLGCCIE

Sequence of entity 2 (C), FASTA

>9JKV_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9JKV_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

>9JKV_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 5 (S), FASTA

>9JKV_5 ScFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
A1EB5	1-propan-2-ylbenzotriazole-5-carboxylic acid	C10 H11 N3 O2	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)
9JKS 3.31 Å, 6O-HCAR3-Gi complex
9JIC 3.4 Å, Cryo-EM Structure of the apo HCAR3-Gi complex

Browse structure collections

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