9IQT: Niacin-HCA2-Gi

structure of niacin-HCA2-Gi. Determined by electron microscopy at 2.9 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,095
Mol. weight: 152.7 kDa
Ligands: NIO
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

9IQT contains 28 α-helices and 65 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-40	7	2
α-helix	46-53	8
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-225	6	2
α-helix	227-229	3
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-254	13
β-strand	263-268	6	2
α-helix	271-280	10
α-helix	296-308	13
β-strand	319-323	5	2
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	30-33	4
α-helix	38-40	3
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	89-94	6	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	148-151	4	7
β-strand	156-160	5	7
β-strand	166-170	5	7
β-strand	176-180	5	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	249-254	6	9
β-strand	259-265	7	9
α-helix	272	1
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
α-helix	30-43	14

Chain E: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	65	1	11
β-strand	68-73	6	11
β-strand	78-83	6	11
β-strand	92-94	3	12
β-strand	95-99	5	13
β-strand	110-111	2	13
β-strand	113	1	11
β-strand	115-119	5	12
β-strand	140-141	2	14
β-strand	146-148	3	15
β-strand	155-161	7	14
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	15
β-strand	185-190	6	15
β-strand	194-195	2	15
β-strand	203-208	6	14
β-strand	211-216	6	14
β-strand	225-231	7	15
α-helix	238	1
β-strand	239	1	15
α-helix	240-242	3
β-strand	243-246	4	15

Chain R: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-50	27
α-helix	51-55	5
α-helix	61-88	28
α-helix	98-129	32
α-helix	141-163	23
β-strand	169-170	2	1
β-strand	175-176	2	1
α-helix	188-217	30
α-helix	220-222	3
α-helix	226-261	36
α-helix	267-291	25
α-helix	292-296	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hydroxycarboxylic acid receptor 2	R	protein	363	Homo sapiens	Q8TDS4 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	352	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	61	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	247	Homo sapiens

Sequence of entity 1 (R), FASTA

>9IQT_1 Hydroxycarboxylic acid receptor 2 (chains R)
MNRHHLQDHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSF
SICHTFQWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKMTGEPDNNRSTSVELTGDPNKTRGAPEALMANSGEPWSPSYLGP
TSP

Sequence of entity 2 (A), FASTA

>9IQT_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGL

Sequence of entity 3 (B), FASTA

>9IQT_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
QSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>9IQT_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
TASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKK
F

Sequence of entity 5 (E), FASTA

>9IQT_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

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

Primary citation

Ligand Recognition and Activation Mechanism of the Alicarboxylic Acid Receptors. Liu, Y., Zhou, Z., Guan, F. et al. J Mol Biol (2024) 436:168795-168795. DOI 10.1016/j.jmb.2024.168795 · 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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