9JID: Niacin-HCAR3-Gi complex

Cryo-EM Structure of the niacin-HCAR3-Gi complex. Determined by electron microscopy at 2.78 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 2.78 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,784
Mol. weight: 153.58 kDa
Ligands: NIO
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9JID contains 32 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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-52	28
α-helix	61-78	18
α-helix	81-83	3
α-helix	97-129	33
α-helix	135-137	3
α-helix	141-159	19
α-helix	161-164	4
β-strand	170	1	1
β-strand	175	1	1
α-helix	188-217	30
α-helix	224-260	37
α-helix	266-269	4
α-helix	271-291	21
α-helix	292-296	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	47-51	5	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
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	222-223	2	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
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-307	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	2
α-helix	46-52	7
β-strand	185-190	6	2
β-strand	195-200	6	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-280	10
α-helix	296-300	5
α-helix	304-309	6
β-strand	319-322	4	2
α-helix	331-351	21

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	53-55	3

Chain S: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-38	6	12
β-strand	46-51	6	12
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-93	2	11
β-strand	94-99	6	12
β-strand	110-111	2	12
β-strand	116-119	4	11
β-strand	129	1	13
β-strand	134	1	14
β-strand	143-148	6	13
β-strand	162-167	6	15
β-strand	173-178	6	15
β-strand	182-183	2	15
β-strand	191-195	5	13
β-strand	199-204	6	13
β-strand	217-219	3	15
β-strand	226-227	2	15
β-strand	232	1	14

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	233	Homo sapiens

Sequence of entity 1 (A), FASTA

>9JID_1 Hydroxycarboxylic acid receptor 3 (chains A)
MNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQNGTANVCISF
SICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKITGEPDNNRSTSVELTGDPNKTRGAPEALIANSGEPWSPSYLGP
TSNNHSKKGHCHQEPASLEKQLGCCIE

Sequence of entity 2 (C), FASTA

>9JID_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9JID_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

>9JID_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 5 (S), FASTA

>9JID_5 ScFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSN
LASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
NIO	Nicotinic acid	C6 H5 N O2	1

Primary citation

Structural basis for ligand recognition of the human hydroxycarboxylic acid receptor HCAR3. Ye, F., Pan, X., Zhang, Z. et al. Cell Rep (2024) 43:114895-114895. DOI 10.1016/j.celrep.2024.114895 · 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
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
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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