8I7V: PDB entry 8I7V

Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer. Determined by electron microscopy at 2.77 Å resolution. Released 7 Feb 2024.

Method: Electron microscopy
Resolution: 2.77 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,374
Mol. weight: 168.53 kDa
Ligands: OJX
Released: 7 Feb 2024

Explore 8I7V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I7V contains 32 α-helices and 67 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: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	18-19	2	1
α-helix	24-26	3
α-helix	30-53	24
α-helix	62-88	27
α-helix	98-129	32
α-helix	135-138	4
α-helix	141-159	19
α-helix	160-162	3
β-strand	169	1	2
β-strand	176	1	2
β-strand	182-183	2	1
α-helix	188-217	30
α-helix	224-260	37
α-helix	266-269	4
α-helix	270-279	10
α-helix	281-290	10
α-helix	291-295	5

Chain B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-39	7	3
α-helix	46-52	7
β-strand	185-190	6	3
β-strand	195-200	6	3
α-helix	208-211	4
β-strand	220-225	6	3
β-strand	263-268	6	3
β-strand	319-323	5	3
α-helix	324-325	2
α-helix	328-351	24

Chain C: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
α-helix	38-39	2
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	146-151	6	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	175-180	6	7
β-strand	187	1	8
β-strand	191-192	2	9
β-strand	198-202	5	9
β-strand	203	1	8
β-strand	207-212	6	9
β-strand	218-223	6	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	250-254	5	10
β-strand	259-264	6	10
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-22	16
α-helix	30-43	14
α-helix	54-55	2
α-helix	56-58	3

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	12	1	13
β-strand	17-25	9	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
α-helix	53-55	3
β-strand	58-60	3	14
β-strand	65	1	12
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-84	7	12
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	111	1	14
β-strand	115-117	3	14
β-strand	119	1	13
β-strand	140-141	2	15
β-strand	146-148	3	16
β-strand	155-161	7	15
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-179	6	16
β-strand	186-190	5	16
β-strand	194-195	2	16
α-helix	196	1
β-strand	203-208	6	15
β-strand	211-216	6	15
α-helix	221-223	3
β-strand	226-231	6	16
α-helix	237	1
β-strand	238-239	2	16
β-strand	243-246	4	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human hydroxycarboxylic acid receptor 2,Hydroxycarboxylic acid receptor 2,Hydroxycarboxylic acid…	A	protein	476	Homo sapiens	P0ABE7 (AlphaFold model), Q8TDS4 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	80	Homo sapiens	P59768
scFv16	E	protein	257	Mus musculus

Sequence of entity 1 (A), FASTA

>8I7V_1 Human hydroxycarboxylic acid receptor 2,Hydroxycarboxylic acid receptor 2,Hydroxycarboxylic acid receptor 2 (chains A)
GPGAPADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDS
PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLEFMNRHHLQ
DHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWKSSRIFLF
NLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTVVAVDRYF
RVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSFSICHTFQ
WHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVFVICFLPS
VVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPSFPNFFST
LINRCLQRKMTGEPDNNRSTSVELTGDPNKTRGAPEALMANSGEPWSPSYLGPTSP

Sequence of entity 2 (B), FASTA

>8I7V_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>8I7V_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>8I7V_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSA

Sequence of entity 5 (E), FASTA

>8I7V_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
OJX	5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid	C6 H7 N2 O3	1

Primary citation

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2. Park, J.H., Kawakami, K., Ishimoto, N. et al. Nat Commun (2023) 14:7150-7150. DOI 10.1038/s41467-023-42764-8 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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