8JIM: PDB entry 8JIM

Cryo-EM structure of MMF bound ketone body receptor HCAR2-Gi signaling complex. Determined by electron microscopy at 2.98 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 2.98 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 9,051
Mol. weight: 162.6 kDa
Ligands: CLR, AW9
Released: 6 Sept 2023

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

Secondary structure: helices and β-sheets

8JIM contains 38 α-helices and 64 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 B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	30-33	4
α-helix	38-43	6
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	70-74	5	2
β-strand	78-82	5	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	146-153	8	4
β-strand	156-161	6	4
β-strand	165-169	5	4
β-strand	176-181	6	4
β-strand	187-192	6	5
β-strand	199-203	5	5
β-strand	207-210	4	5
β-strand	220-223	4	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	303-308	6	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-22	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain D: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-26	15
β-strand	34-40	7	8
α-helix	46-53	8
β-strand	185-191	7	8
β-strand	194-200	7	8
α-helix	208-210	3
β-strand	220-226	7	8
α-helix	227-229	3
α-helix	232	1
β-strand	233	1	9
α-helix	234	1
β-strand	241	1	9
α-helix	242-254	13
β-strand	263-269	7	8
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	8
α-helix	333-350	18

Chain E: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	16
β-strand	18-19	2	16
α-helix	26-53	28
α-helix	65-77	13
α-helix	80-88	9
α-helix	97-100	4
α-helix	107-110	4
α-helix	112-119	8
α-helix	121-129	9
α-helix	136-138	3
α-helix	141-156	16
α-helix	160-162	3
β-strand	169-170	2	17
β-strand	175-176	2	17
α-helix	188-192	5
α-helix	198-213	16
α-helix	225-243	19
α-helix	246-260	15
α-helix	266-270	5
α-helix	272-279	8
α-helix	285-288	4

Chain S: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-59	2	12
β-strand	68-71	4	10
β-strand	78-83	6	10
β-strand	92-99	8	12
β-strand	115-117	3	12
β-strand	118-119	2	11
β-strand	140-141	2	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
β-strand	203-208	6	13
β-strand	211-216	6	13
β-strand	225-231	7	14
α-helix	237	1
β-strand	239	1	14
α-helix	240-242	3
β-strand	243-246	4	14

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	E	protein	397	Homo sapiens	Q8TDS4 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8JIM_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

>8JIM_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (D), FASTA

>8JIM_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains D)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (S), FASTA

>8JIM_4 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAENLYFQGHHHHHHHH

Sequence of entity 5 (E), FASTA

>8JIM_5 Hydroxycarboxylic acid receptor 2 (chains E)
MKTIIALSYIFCLVFADYKDDDDAHHHHHHHHHHMNRHHLQDHFLEIDKKNCCVFRDDFI
VKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWKSSRIFLFNLAVADFLLIICLPFLMDN
YVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTVVAVDRYFRVVHPHHALNKISNRTAAI
ISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSFSICHTFQWHEAMFLLEFFLPLGIILF
CSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVFVICFLPSVVVRIRIFWLLHTSGTQNC
EVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPSFPNFFSTLINRCLQRKMTGEPDNNRS
TSVELTGDPNKTRGAPEALMANSGEPWSPSYLGPTSP

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
AW9	(2Z)-4-methoxy-4-oxobut-2-enoic acid	C5 H6 O4	1

Primary citation

Biased allosteric activation of ketone body receptor HCAR2 suppresses inflammation. Zhao, C., Wang, H., Liu, Y. et al. Mol Cell (2023) 83:3171. DOI 10.1016/j.molcel.2023.07.030 · 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

Browse structure collections

About this viewer

MolViewer shows 8JIM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.