7YU5: PDB entry 7YU5
Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state1. Determined by electron microscopy at 3.7 Å resolution. Released 5 Oct 2022.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organisms
- Rattus norvegicus, Homo sapiens, Bos taurus
- Chains
- 5
- Atoms
- 8,787
- Mol. weight
- 157.78 kDa
- Ligands
- K6L
- Released
- 5 Oct 2022
Explore 7YU5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7YU5 contains 34 α-helices and 58 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: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-32 | 26 | |
| β-strand | 33-40 | 8 | 8 |
| α-helix | 46-53 | 8 | |
| β-strand | 183-191 | 9 | 8 |
| β-strand | 194-203 | 10 | 8 |
| α-helix | 208-211 | 4 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 8 |
| α-helix | 227-229 | 3 | |
| α-helix | 242-254 | 13 | |
| β-strand | 263-269 | 7 | 8 |
| α-helix | 271-278 | 8 | |
| α-helix | 296-308 | 13 | |
| β-strand | 319-323 | 5 | 8 |
| α-helix | 331-350 | 20 | |
Chain B: 6 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-24 | 21 | |
| α-helix | 30-33 | 4 | |
| α-helix | 34-36 | 3 | |
| α-helix | 38-39 | 2 | |
| 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 |
| α-helix | 95 | 1 | |
| β-strand | 100-105 | 6 | 3 |
| β-strand | 111-116 | 6 | 3 |
| β-strand | 121-125 | 5 | 3 |
| β-strand | 134-139 | 6 | 3 |
| β-strand | 146-151 | 6 | 4 |
| β-strand | 157-161 | 5 | 4 |
| β-strand | 166-170 | 5 | 4 |
| β-strand | 175-180 | 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 | 260-264 | 5 | 6 |
| α-helix | 272-273 | 2 | |
| β-strand | 275-278 | 4 | 7 |
| β-strand | 284-288 | 5 | 7 |
| β-strand | 294-298 | 5 | 7 |
| β-strand | 304-308 | 5 | 7 |
| β-strand | 318-320 | 3 | 1 |
| β-strand | 327-329 | 3 | 1 |
| β-strand | 335-339 | 5 | 1 |
Chain G: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-23 | 15 | |
| α-helix | 30-43 | 14 | |
| α-helix | 45-47 | 3 | |
| α-helix | 53-55 | 3 | |
| α-helix | 56-58 | 3 | |
Chain R: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-36 | 7 | |
| α-helix | 47-76 | 30 | |
| α-helix | 78-80 | 3 | |
| α-helix | 83-105 | 23 | |
| α-helix | 110-115 | 6 | |
| α-helix | 118-151 | 34 | |
| α-helix | 162-184 | 23 | |
| α-helix | 204-238 | 35 | |
| α-helix | 252-283 | 32 | |
| α-helix | 293-310 | 18 | |
| α-helix | 316-320 | 5 | |
Chain S: 3 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 9 |
| β-strand | 10-12 | 3 | 10 |
| β-strand | 19-24 | 6 | 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 |
| α-helix | 74-76 | 3 | |
| β-strand | 78-83 | 6 | 9 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 10 |
| β-strand | 110-111 | 2 | 10 |
| β-strand | 115-119 | 5 | 10 |
| β-strand | 140-141 | 2 | 11 |
| β-strand | 147-148 | 2 | 12 |
| β-strand | 155-161 | 7 | 11 |
| β-strand | 166 | 1 | 13 |
| β-strand | 172 | 1 | 13 |
| β-strand | 174-179 | 6 | 14 |
| β-strand | 186-189 | 4 | 14 |
| β-strand | 203-208 | 6 | 11 |
| β-strand | 211-216 | 6 | 11 |
| β-strand | 226-231 | 6 | 14 |
| β-strand | 239 | 1 | 14 |
| β-strand | 243-244 | 2 | 14 |
| β-strand | 245-246 | 2 | 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 | 351 | Rattus norvegicus | P54311 (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(O) subunit gamma-2 | G | protein | 68 | Bos taurus | P63212 (AlphaFold model) |
| Lysophosphatidic acid receptor 1 | R | protein | 379 | Homo sapiens | Q92633 (AlphaFold model) |
| scFv16 | S | protein | 260 | Mus musculus | |
Sequence of entity 1 (B), FASTA
>7YU5_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 2 (A), FASTA
>7YU5_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
Sequence of entity 3 (G), FASTA
>7YU5_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFS
Sequence of entity 4 (R), FASTA
>7YU5_4 Lysophosphatidic acid receptor 1 (chains R)
DYKDDDDAMGAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKL
VMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGP
NTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVI
WTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGY
VRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLA
YEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEGSDRSASSLNHT
ILAGVHSNDHSVVENLYFQ
Sequence of entity 5 (S), FASTA
>7YU5_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAASSEDLYFQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| K6L | [(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen… | C20 H34 N O6 P | 1 |
Primary citation
Structure of the active G i -coupled human lysophosphatidic acid receptor 1 complexed with a potent agonist. Akasaka, H., Tanaka, T., Sano, F.K. et al. Nat Commun (2022) 13:5417-5417. DOI 10.1038/s41467-022-33121-2 · PubMed
Other PDB entries of the same protein (UniProt P54311 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
- 9EJZ 2.06 Å, Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine…
- 9IJE 2.34 Å, Epinephrine-activated human beta3 adrenergic receptor
- 8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
- 8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
- 22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
- 7MBY 2.44 Å, Human Cholecystokinin 1 receptor (CCK1R) Gq chimera (mGsqi) complex
- 9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
- 8JIS 2.46 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist peptide15-bound human GLP-1R-Gs complex
- 9M0R 2.47 Å, Structure of neuropeptide FF receptor 1 complex with NPVF
- 8YKV 2.48 Å, Cryo-EM structure of succinate receptor SUCR1 bound to compound 31
- 9M1O 2.49 Å, Cryo-EM structures of NPFFR2 complex with neuropeptide FF
Browse structure collections
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