8YKX: Succinate receptor SUCR1
Cryo-EM structure of succinate receptor SUCR1 bound to maleic acid. Determined by electron microscopy at 2.69 Å resolution. Released 29 May 2024.
- Method
- Electron microscopy
- Resolution
- 2.69 Å
- Organisms
- Homo sapiens, Rattus norvegicus, synthetic construct
- Chains
- 5
- Atoms
- 8,710
- Mol. weight
- 150.85 kDa
- Ligands
- MAE
- Released
- 29 May 2024
Explore 8YKX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YKX contains 40 α-helices and 60 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 | 7-31 | 25 | |
| β-strand | 33-39 | 7 | 1 |
| α-helix | 46-49 | 4 | |
| α-helix | 50-52 | 3 | |
| β-strand | 185-191 | 7 | 1 |
| β-strand | 194-200 | 7 | 1 |
| α-helix | 208-211 | 4 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 1 |
| α-helix | 242-254 | 13 | |
| α-helix | 257-259 | 3 | |
| 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 | 330-350 | 21 | |
Chain B: 3 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-25 | 21 | |
| α-helix | 30-34 | 5 | |
| α-helix | 38-41 | 4 | |
| β-strand | 43 | 1 | 2 |
| β-strand | 47-51 | 5 | 3 |
| β-strand | 58-63 | 6 | 4 |
| β-strand | 69-74 | 6 | 4 |
| β-strand | 78-83 | 6 | 4 |
| β-strand | 88-94 | 7 | 4 |
| β-strand | 100-105 | 6 | 5 |
| β-strand | 111-116 | 6 | 5 |
| β-strand | 120-125 | 6 | 5 |
| β-strand | 134-140 | 7 | 5 |
| β-strand | 146-151 | 6 | 6 |
| β-strand | 156-161 | 6 | 6 |
| β-strand | 166-170 | 5 | 6 |
| β-strand | 176-180 | 5 | 6 |
| β-strand | 187-192 | 6 | 7 |
| β-strand | 198-203 | 6 | 7 |
| β-strand | 207-212 | 6 | 7 |
| β-strand | 217-223 | 7 | 7 |
| β-strand | 229-234 | 6 | 8 |
| β-strand | 240-245 | 6 | 8 |
| β-strand | 250-254 | 5 | 8 |
| β-strand | 259-264 | 6 | 8 |
| β-strand | 273-278 | 6 | 2 |
| β-strand | 284-289 | 6 | 2 |
| β-strand | 294-298 | 5 | 2 |
| β-strand | 304-308 | 5 | 2 |
| β-strand | 317-320 | 4 | 3 |
| β-strand | 327-330 | 4 | 3 |
| β-strand | 336-339 | 4 | 3 |
Chain E: 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 |
| 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 | 65 | 1 | 9 |
| β-strand | 68-73 | 6 | 9 |
| β-strand | 78-84 | 7 | 9 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 10 |
| β-strand | 110-111 | 2 | 10 |
| β-strand | 115-119 | 5 | 10 |
| α-helix | 137-139 | 3 | |
| 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 |
| α-helix | 196 | 1 | |
| β-strand | 203-208 | 6 | 11 |
| β-strand | 211-216 | 6 | 11 |
| β-strand | 226-231 | 6 | 12 |
| β-strand | 239 | 1 | 12 |
| β-strand | 243-246 | 4 | 12 |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-24 | 16 | |
| α-helix | 30-43 | 14 | |
| α-helix | 45-47 | 3 | |
| α-helix | 53-55 | 3 | |
Chain R: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-20 | 9 | |
| α-helix | 21-25 | 5 | |
| α-helix | 26-48 | 23 | |
| α-helix | 57-73 | 17 | |
| α-helix | 76-85 | 10 | |
| α-helix | 92-125 | 34 | |
| α-helix | 132-134 | 3 | |
| α-helix | 136-154 | 19 | |
| α-helix | 155-157 | 3 | |
| α-helix | 181-192 | 12 | |
| α-helix | 193-197 | 5 | |
| α-helix | 198-216 | 19 | |
| α-helix | 225-226 | 2 | |
| α-helix | 228-258 | 31 | |
| α-helix | 270-285 | 16 | |
| α-helix | 287-292 | 6 | |
| α-helix | 293-297 | 5 | |
| α-helix | 300-308 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Succinate receptor 1 | R | protein | 334 | Homo sapiens | Q9BXA5 (AlphaFold model) |
| 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 | 340 | Rattus norvegicus | P54311 (AlphaFold model) |
| Antibody fragment ScFv16 | E | protein | 247 | synthetic construct | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 71 | Bos taurus | P63212 (AlphaFold model) |
Sequence of entity 1 (R), FASTA
>8YKX_1 Succinate receptor 1 (chains R)
MLGIMAWNATCKNWLAAEAALEKYYLSIFYGIEFVVGVLGNTIVVYGYIFSLKNWNSSNI
YLFNLSVSDLAFLCTLPMLIRSYANGNWIYGDVLCISNRYVLHANLYTSILFLTFISIDR
YLIIKYPFREHLLQKKEFAILISLAIWVLVTLELLPILPLINPVITDNGTTCNDFASSGD
PNYNLIYSMCLTLLGFLIPLFVMCFFYYKIALFLKQRNRQVATALPLEKPLNLVIMAVVI
FSVLFTPYHVMRNVRIASRLGSWKQYQCTQVVINSFYIVTRPLAFLNSVINPVFYFLLGD
HFRDMLMNQLRHNFKSLTSFSRWAHELLLSFREK
Sequence of entity 2 (A), FASTA
>8YKX_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF
Sequence of entity 3 (B), FASTA
>8YKX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 4 (E), FASTA
>8YKX_4 Antibody fragment ScFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSS
GGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL
Sequence of entity 5 (G), FASTA
>8YKX_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MAE | Maleic acid | C4 H4 O4 | 1 |
Primary citation
Molecular basis of ligand recognition and activation of the human succinate receptor SUCR1. Li, C., Liu, H., Li, J. et al. Cell Res (2024) 34:594-596. DOI 10.1038/s41422-024-00984-7 · PubMed
Other PDB entries of the same protein (UniProt Q9BXA5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8YKV 2.48 Å, Cryo-EM structure of succinate receptor SUCR1 bound to compound 31
- 8YKW 2.75 Å, Cryo-EM structure of succinate receptor SUCR1 bound to succinic acid
- 8JPN 2.9 Å, Cryo-EM structure of succinate receptor bound to cis-epoxysuccinic acid coupling to Gi
- 8WOG 2.97 Å, Cryo-EM structure of SUCR1 in complex with succinate and Gi protein
- 8WP1 3.15 Å, Cryo-EM structure of SUCR1 in complex with cis-epoxysuccinic acid and Gi proteins
- 8JPP 3.2 Å, Cryo-EM structure of succinate receptor bound to succinate acid coupling MiniGsq
Browse structure collections
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