8YYX: OXGR1
Cryo-EM structure of OXGR1 bound to leukotriene E4 and Gq proteins. Determined by electron microscopy at 2.84 Å resolution. Released 9 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 2.84 Å
- Organisms
- Vicugna pacos, Homo sapiens
- Chains
- 5
- Atoms
- 9,103
- Mol. weight
- 151.15 kDa
- Ligands
- A1D7P, CLR
- Released
- 9 Apr 2025
Explore 8YYX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YYX contains 34 α-helices and 63 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: 3 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 1 |
| β-strand | 10-12 | 3 | 2 |
| β-strand | 17-25 | 9 | 1 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 2 |
| β-strand | 45-51 | 7 | 2 |
| β-strand | 58-60 | 3 | 2 |
| β-strand | 68-73 | 6 | 1 |
| β-strand | 78-84 | 7 | 1 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 2 |
| β-strand | 110-111 | 2 | 2 |
| β-strand | 113 | 1 | 1 |
| β-strand | 115-119 | 5 | 2 |
| β-strand | 140-141 | 2 | 3 |
| β-strand | 146-148 | 3 | 4 |
| β-strand | 155-161 | 7 | 3 |
| β-strand | 166 | 1 | 5 |
| β-strand | 172 | 1 | 5 |
| β-strand | 174-179 | 6 | 4 |
| β-strand | 186-190 | 5 | 4 |
| β-strand | 194-195 | 2 | 4 |
| α-helix | 196 | 1 | |
| β-strand | 203-207 | 5 | 3 |
| β-strand | 211-216 | 6 | 3 |
| β-strand | 225-231 | 7 | 4 |
| β-strand | 239 | 1 | 4 |
| β-strand | 243-246 | 4 | 4 |
Chain B: 3 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-24 | 22 | |
| α-helix | 30-33 | 4 | |
| α-helix | 38-39 | 2 | |
| β-strand | 47-51 | 5 | 6 |
| β-strand | 58-63 | 6 | 7 |
| β-strand | 69-74 | 6 | 7 |
| β-strand | 78-83 | 6 | 7 |
| β-strand | 89-94 | 6 | 7 |
| β-strand | 100-105 | 6 | 8 |
| β-strand | 111-116 | 6 | 8 |
| β-strand | 120-125 | 6 | 8 |
| β-strand | 134-140 | 7 | 8 |
| β-strand | 146-153 | 8 | 9 |
| β-strand | 156-161 | 6 | 9 |
| β-strand | 165-170 | 6 | 9 |
| β-strand | 175-181 | 7 | 9 |
| β-strand | 187-192 | 6 | 10 |
| β-strand | 198-203 | 6 | 10 |
| β-strand | 207-212 | 6 | 10 |
| β-strand | 217-223 | 7 | 10 |
| β-strand | 229-234 | 6 | 11 |
| β-strand | 240-245 | 6 | 11 |
| β-strand | 250-254 | 5 | 11 |
| β-strand | 259-264 | 6 | 11 |
| β-strand | 273-278 | 6 | 12 |
| β-strand | 284-289 | 6 | 12 |
| β-strand | 294-298 | 5 | 12 |
| β-strand | 304-308 | 5 | 12 |
| β-strand | 315-320 | 6 | 6 |
| β-strand | 327-331 | 5 | 6 |
| β-strand | 335-339 | 5 | 6 |
Chain C: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-31 | 25 | |
| β-strand | 34-40 | 7 | 13 |
| β-strand | 185-190 | 6 | 13 |
| β-strand | 195-200 | 6 | 13 |
| α-helix | 208-210 | 3 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 13 |
| α-helix | 227-230 | 4 | |
| β-strand | 233 | 1 | 14 |
| β-strand | 241 | 1 | 14 |
| α-helix | 242-254 | 13 | |
| β-strand | 263-269 | 7 | 13 |
| α-helix | 271-275 | 5 | |
| α-helix | 276-279 | 4 | |
| α-helix | 283-285 | 3 | |
| α-helix | 296-308 | 13 | |
| β-strand | 319-323 | 5 | 13 |
| α-helix | 330-350 | 21 | |
Chain D: 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 E: 13 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-34 | 6 | |
| α-helix | 36-61 | 26 | |
| α-helix | 67-84 | 18 | |
| α-helix | 86-94 | 9 | |
| α-helix | 103-136 | 34 | |
| α-helix | 147-165 | 19 | |
| α-helix | 166-171 | 6 | |
| β-strand | 174-176 | 3 | 15 |
| β-strand | 181-183 | 3 | 15 |
| α-helix | 195-206 | 12 | |
| α-helix | 208-226 | 19 | |
| α-helix | 234-267 | 34 | |
| α-helix | 274-299 | 26 | |
| α-helix | 300-304 | 5 | |
| α-helix | 307-321 | 15 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| scFV16 | A | protein | 247 | Vicugna pacos | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 339 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q)… | C | protein | 354 | Homo sapiens | P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | D | protein | 71 | Homo sapiens | P59768 (AlphaFold model) |
| 2-oxoglutarate receptor 1 | E | protein | 337 | Homo sapiens | Q96P68 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>8YYX_1 scFV16 (chains A)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL
Sequence of entity 2 (B), FASTA
>8YYX_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 3 (C), FASTA
>8YYX_3 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTENIRFVFAAVKDTILQLNLKEYNLV
Sequence of entity 4 (D), FASTA
>8YYX_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 5 (E), FASTA
>8YYX_5 2-oxoglutarate receptor 1 (chains E)
MNEPLDYLANASDFPDYAAAFGNCTDENIPLKMHYLPVIYGIIFLVGFPGNAVVISTYIF
KMRPWKSSTIIMLNLACTDLLYLTSLPFLIHYYASGENWIFGDFMCKFIRFSFHFNLYSS
ILFLTCFSIFRYCVIIHPMSCFSIHKTRCAVVACAVVWIISLVAVIPMTFLITSTNRTNR
SACLDLTSSDELNTIKWYNLILTATTFCLPLVIVTLCYTTIIHTLTHGLQTDSCLKQKAR
RLTILLLLAFYVCFLPFHILRVIRIESRLLSISCSIENQIHEAYIVSRPLAALNTFGNLL
LYVVVSDNFQQAVCSTVRCKVSGNLEQAKKISYSNNP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| A1D7P | (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidan… | C23 H37 N O5 S | 1 |
| CLR | Cholesterol | C27 H46 O | 1 |
Primary citation
Molecular insights into ligand recognition and signaling of OXGR1. Liu, A., Liu, Y., Long, Y. et al. Nat Commun (2025) 16:11205-11205. DOI 10.1038/s41467-025-67101-z · 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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