8JZ7: MK-6892-bound HCAR2

Cryo-EM structure of MK-6892-bound HCAR2 in complex with Gi protein. Determined by electron microscopy at 2.6 Å resolution. Released 4 Oct 2023.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 9,042
Mol. weight: 162.47 kDa
Ligands: FI7
Released: 4 Oct 2023

Explore 8JZ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JZ7 contains 34 α-helices and 62 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: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	14
β-strand	17-18	2	14
α-helix	30-54	25
α-helix	67-78	12
α-helix	81-88	8
α-helix	99-110	12
α-helix	112-118	7
α-helix	120-129	10
α-helix	135-138	4
α-helix	152-159	8
β-strand	169	1	15
β-strand	176	1	15
α-helix	188-217	30
α-helix	224-226	3
α-helix	228-238	11
α-helix	245-260	16
α-helix	266-269	4
α-helix	270-279	10
α-helix	280-282	3
α-helix	286-291	6
α-helix	292-296	5

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-23	22
α-helix	30-34	5
α-helix	38-40	3
β-strand	47-52	6	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	89-94	6	2
β-strand	102-105	4	3
β-strand	111-115	5	3
β-strand	120-125	6	3
β-strand	134-140	7	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-223	6	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	260-264	5	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	335-339	5	1

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-21	15
α-helix	30-43	14

Chain D: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-40	8	8
α-helix	46-53	8
β-strand	185-190	6	8
β-strand	195-200	6	8
α-helix	208-210	3
α-helix	213-215	3
β-strand	220-226	7	8
α-helix	242-254	13
β-strand	263-269	7	8
α-helix	272-279	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	8
α-helix	331-351	21

Chain S: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	15-25	11	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-85	8	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	110	1	10
β-strand	115-119	5	10
β-strand	140-141	2	11
β-strand	146-148	3	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	186-190	5	12
β-strand	194-195	2	12
β-strand	203-208	6	11
β-strand	211-216	6	11
β-strand	226-231	6	12
α-helix	237	1
β-strand	239	1	12
β-strand	243-246	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	356	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	D	protein	354	Homo sapiens	P63096 (AlphaFold model)
scFv16	S	protein	266	Mus musculus
Hydroxycarboxylic acid receptor 2	A	protein	397	Homo sapiens	Q8TDS4 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8JZ7_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQ
MRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCA
YAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDT
TCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTG
HESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRL
LLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (C), FASTA

>8JZ7_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (D), FASTA

>8JZ7_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains D)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (S), FASTA

>8JZ7_4 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAENLYFQGHHHHHHHH

Sequence of entity 5 (A), FASTA

>8JZ7_5 Hydroxycarboxylic acid receptor 2 (chains A)
MKTIIALSYIFCLVFADYKDDDDAHHHHHHHHHHMNRHHLQDHFLEIDKKNCCVFRDDFI
VKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWKSSRIFLFNLAVADFLLIICLPFLMDN
YVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTVVAVDRYFRVVHPHHALNKISNRTAAI
ISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSFSICHTFQWHEAMFLLEFFLPLGIILF
CSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVFVICFLPSVVVRIRIFWLLHTSGTQNC
EVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPSFPNFFSTLINRCLQRKMTGEPDNNRS
TSVELTGDPNKTRGAPEALMANSGEPWSPSYLGPTSP

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

Orthosteric ligand selectivity and allosteric probe dependence at Hydroxycarboxylic acid receptor HCAR2. Cheng, L., Sun, S., Wang, H. et al. Signal Transduct Target Ther (2023) 8:364-364. DOI 10.1038/s41392-023-01625-y · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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