8J6J: PDB entry 8J6J

Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound with GSK256073. Determined by electron microscopy at 2.8 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,979
Mol. weight: 170.88 kDa
Ligands: OKL
Released: 10 Jan 2024

Explore 8J6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J6J contains 33 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	34-39	6	1
α-helix	43-51	9
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	202-204	3
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-230	4
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 3 helices, 28 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	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
β-strand	276-278	3	8
β-strand	284-288	5	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	317-320	4	2
β-strand	327-330	4	2
β-strand	336-339	4	2

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	30-35	6

Chain H: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	59-60	2	11
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	93-99	7	11
β-strand	111	1	11
β-strand	115-116	2	11
β-strand	117-119	3	10
β-strand	140-142	3	12
β-strand	146-148	3	13
β-strand	155-161	7	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
α-helix	196	1
β-strand	203-207	5	12
β-strand	211-216	6	12
α-helix	221-223	3
β-strand	225-231	7	13
β-strand	239	1	13
β-strand	243-246	4	13

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	26-52	27
α-helix	61-88	28
α-helix	97-130	34
α-helix	132-135	4
α-helix	136-138	3
α-helix	141-159	19
α-helix	160-162	3
β-strand	170-171	2	15
β-strand	174-175	2	15
α-helix	188-218	31
α-helix	224-256	33
α-helix	270-294	25
α-helix	295-297	3
α-helix	300-307	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	370	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	70	Homo sapiens	P59768 (AlphaFold model)
Scfv16	H	protein	247	Homo sapiens
Hydroxycarboxylic acid receptor 2,hydroxycarboxylic acid receptor 2	R	protein	488	Homo sapiens	Q8TDS4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8J6J_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8J6J_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSGV
SGWRLFKKIS

Sequence of entity 3 (G), FASTA

>8J6J_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 4 (H), FASTA

>8J6J_4 Scfv16 (chains H)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 5 (R), FASTA

>8J6J_5 Hydroxycarboxylic acid receptor 2,hydroxycarboxylic acid receptor 2 (chains R)
MNRHHLQDHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSF
SICHTFQWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKMTGEPDNNRSTSVEVFTLEDFVGDWEQTAAYNLDQVLEQGGVSS
LLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFK
VILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSM
LFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
OKL	8-chloranyl-3-pentyl-7H-purine-2,6-dione	C10 H13 Cl N4 O2	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 P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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