8J6I: Hydroxycarboxylic acid receptor 2

Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound MK-6892. Determined by electron microscopy at 2.92 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,801
Mol. weight: 146.98 kDa
Ligands: FI7
Released: 3 Apr 2024

Explore 8J6I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J6I contains 32 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: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	34-40	7	2
α-helix	43-52	10
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	227-231	5
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	2
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-309	14
β-strand	319	1	2
β-strand	322-323	2	2
α-helix	331-351	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	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	122-125	4	5
β-strand	134-137	4	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	176-180	5	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	220-222	3	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	260-264	5	8
β-strand	273-278	6	9
β-strand	284-289	6	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 G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
α-helix	30-43	14

Chain H: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	59-60	2	12
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	93-99	7	12
β-strand	111	1	12
β-strand	115	1	12
β-strand	117-119	3	11
β-strand	140-142	3	13
β-strand	146-148	3	14
β-strand	155-161	7	13
β-strand	166	1	15
β-strand	172	1	15
β-strand	174-179	6	14
β-strand	186-190	5	14
β-strand	194-195	2	14
α-helix	196	1
β-strand	203-207	5	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	225-231	7	14
β-strand	243-246	4	14

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-54	29
α-helix	64-78	15
α-helix	80-88	9
α-helix	97-129	33
α-helix	141-159	19
α-helix	160-164	5
α-helix	168	1
β-strand	169-170	2	1
β-strand	175-176	2	1
α-helix	188-218	31
α-helix	227-244	18
α-helix	246-260	15
α-helix	272-279	8
α-helix	281-294	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hydroxycarboxylic acid receptor 2	R	protein	311	Homo sapiens	Q8TDS4 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	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	H	protein	247	Homo sapiens

Sequence of entity 1 (R), FASTA

>8J6I_1 Hydroxycarboxylic acid receptor 2 (chains R)
MNRHHLQDHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSF
SICHTFQWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINR

Sequence of entity 2 (A), FASTA

>8J6I_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>8J6I_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>8J6I_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 5 (H), FASTA

>8J6I_5 Scfv16 (chains H)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
FI7	2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]a…	C19 H22 N4 O5	1

Primary citation

Molecular recognition of niacin and lipid-lowering drugs by the human hydroxycarboxylic acid receptor 2. Zhu, S., Yuan, Q., Li, X. et al. Cell Rep (2023) 42:113406-113406. DOI 10.1016/j.celrep.2023.113406 · PubMed

Other PDB entries of the same protein (UniProt Q8TDS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8J6P 2.55 Å, Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex
8J6Q 2.6 Å, Cryo-EM structure of the 3-HB and compound 9n-bound human HCAR2-Gi1 complex
8JZ7 2.6 Å, Cryo-EM structure of MK-6892-bound HCAR2 in complex with Gi protein
9IZC 2.68 Å, Cryo-EM structure of human HCAR2-Gi complex with MK1903
8IJA 2.69 Å, Cryo-EM structure of human HCAR2-Gi complex with niacin
7ZL9 2.7 Å, Crystal structure of human GPCR Niacin receptor (HCA2)
7ZLY 2.7 Å, Crystal structure of human GPCR Niacin receptor (HCA2) expressed from Spodoptera…
9JKY 2.72 Å, acifran-HCAR2-Gi complex
9KT8 2.73 Å, Cryo-EM structure of HCA2-Gi complex with acifran
8J6R 2.76 Å, Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex
8I7V 2.77 Å, Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 in complex…
8J6J 2.8 Å, Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound with…

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