9JIC: Apo HCAR3-Gi complex

Cryo-EM Structure of the apo HCAR3-Gi complex. Determined by electron microscopy at 3.4 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,682
Mol. weight: 153.45 kDa
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9JIC contains 25 α-helices and 57 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: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	30-54	25
α-helix	61-77	17
α-helix	80-88	9
α-helix	98-129	32
α-helix	141-163	23
α-helix	173-177	5
α-helix	189-216	28
α-helix	225-260	36
α-helix	266-297	32

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
α-helix	30-33	4
α-helix	38-39	2
β-strand	47	1	3
β-strand	51	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
α-helix	95	1
β-strand	103-105	3	5
β-strand	111-114	4	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	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	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	276-278	3	9
β-strand	284-287	4	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	36-39	4	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	220-223	4	1
β-strand	226	1	2
α-helix	242-254	13
β-strand	263-268	6	1
β-strand	269	1	2
α-helix	271-280	10
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	331-350	20

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-44	15
α-helix	56-58	3

Chain S: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-117	3	11
β-strand	146-148	3	12
β-strand	154	1	13
β-strand	160	1	13
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
β-strand	193-196	4	12
β-strand	199-202	4	12
β-strand	214-219	6	14
β-strand	231-232	2	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

>9JIC_1 Hydroxycarboxylic acid receptor 3 (chains A)
MNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQNGTANVCISF
SICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKITGEPDNNRSTSVELTGDPNKTRGAPEALIANSGEPWSPSYLGP
TSNNHSKKGHCHQEPASLEKQLGCCIE

Sequence of entity 2 (C), FASTA

>9JIC_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9JIC_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

>9JIC_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 5 (S), FASTA

>9JIC_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSN
LASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

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
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
9JKS 3.31 Å, 6O-HCAR3-Gi complex

Browse structure collections

About this viewer

MolViewer shows 9JIC 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.