8JHY: PDB entry 8JHY
Cryo-EM structure of compound 9n bound ketone body receptor HCAR2-Gi signaling complex. Determined by electron microscopy at 2.87 Å resolution. Released 6 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 2.87 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 5
- Atoms
- 9,073
- Mol. weight
- 162.9 kDa
- Ligands
- CLR, IX8
- Released
- 6 Sept 2023
Explore 8JHY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8JHY contains 38 α-helices and 66 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: 18 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-12 | 2 | 17 |
| β-strand | 18-19 | 2 | 17 |
| α-helix | 26-54 | 29 | |
| α-helix | 66-71 | 6 | |
| α-helix | 75-78 | 4 | |
| α-helix | 80-88 | 9 | |
| α-helix | 99-106 | 8 | |
| α-helix | 112-119 | 8 | |
| α-helix | 121-129 | 9 | |
| α-helix | 135-138 | 4 | |
| α-helix | 144-159 | 16 | |
| α-helix | 160-162 | 3 | |
| β-strand | 169-170 | 2 | 18 |
| β-strand | 175-176 | 2 | 18 |
| β-strand | 182-183 | 2 | 17 |
| α-helix | 189-214 | 26 | |
| α-helix | 231-238 | 8 | |
| α-helix | 246-260 | 15 | |
| α-helix | 266-270 | 5 | |
| α-helix | 272-279 | 8 | |
| α-helix | 280-282 | 3 | |
| α-helix | 286-291 | 6 | |
| α-helix | 292-296 | 5 | |
Chain B: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| α-helix | 30-34 | 5 | |
| α-helix | 38-43 | 6 | |
| β-strand | 47-51 | 5 | 1 |
| β-strand | 58-63 | 6 | 2 |
| β-strand | 69-74 | 6 | 2 |
| β-strand | 78-83 | 6 | 2 |
| β-strand | 88-94 | 7 | 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 | 176-181 | 6 | 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 | 259-264 | 6 | 6 |
| α-helix | 272 | 1 | |
| 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 | Sheet |
|---|
| α-helix | 7-22 | 16 | |
| α-helix | 30-42 | 13 | |
| α-helix | 45-47 | 3 | |
| α-helix | 53-55 | 3 | |
Chain D: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-30 | 22 | |
| β-strand | 34-39 | 6 | 8 |
| α-helix | 46-51 | 6 | |
| β-strand | 185-190 | 6 | 8 |
| β-strand | 195-200 | 6 | 8 |
| α-helix | 208-210 | 3 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 8 |
| β-strand | 233 | 1 | 9 |
| β-strand | 241 | 1 | 9 |
| α-helix | 242-254 | 13 | |
| α-helix | 257-259 | 3 | |
| β-strand | 263-269 | 7 | 8 |
| α-helix | 271-280 | 10 | |
| α-helix | 296-308 | 13 | |
| β-strand | 319-323 | 5 | 8 |
| α-helix | 330-350 | 21 | |
Chain S: 3 helices, 25 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 | 33-37 | 5 | 12 |
| β-strand | 47-51 | 5 | 12 |
| β-strand | 58-59 | 2 | 12 |
| β-strand | 68-73 | 6 | 10 |
| β-strand | 78-83 | 6 | 10 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-94 | 3 | 13 |
| β-strand | 95-99 | 5 | 12 |
| β-strand | 115-117 | 3 | 13 |
| β-strand | 118-119 | 2 | 11 |
| β-strand | 141 | 1 | 14 |
| β-strand | 146-148 | 3 | 15 |
| β-strand | 155-160 | 6 | 14 |
| β-strand | 166 | 1 | 16 |
| β-strand | 172 | 1 | 16 |
| β-strand | 174-179 | 6 | 15 |
| β-strand | 186-190 | 5 | 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 | 237 | 1 | |
| β-strand | 239 | 1 | 15 |
| β-strand | 243-246 | 4 | 15 |
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
>8JHY_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
>8JHY_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 3 (D), FASTA
>8JHY_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains D)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF
Sequence of entity 4 (S), FASTA
>8JHY_4 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAENLYFQGHHHHHHHH
Sequence of entity 5 (A), FASTA
>8JHY_5 Hydroxycarboxylic acid receptor 2 (chains A)
MKTIIALSYIFCLVFADYKDDDDAHHHHHHHHHHMNRHHLQDHFLEIDKKNCCVFRDDFI
VKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWKSSRIFLFNLAVADFLLIICLPFLMDN
YVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTVVAVDRYFRVVHPHHALNKISNRTAAI
ISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSFSICHTFQWHEAMFLLEFFLPLGIILF
CSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVFVICFLPSVVVRIRIFWLLHTSGTQNC
EVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPSFPNFFSTLINRCLQRKMTGEPDNNRS
TSVELTGDPNKTRGAPEALMANSGEPWSPSYLGPTSP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 1 |
| IX8 | 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]py… | C26 H28 N4 O2 | 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
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