7XXH: Purinergic receptor P2Y1R
Cryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11. Determined by electron microscopy at 2.9 Å resolution. Released 7 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 8,847
- Mol. weight
- 160.6 kDa
- Ligands
- 6AD
- Released
- 7 Jun 2023
Explore 7XXH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7XXH contains 27 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: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-30 | 24 | |
| β-strand | 33-40 | 8 | 3 |
| α-helix | 42-44 | 3 | |
| α-helix | 46-57 | 12 | |
| β-strand | 185 | 1 | 3 |
| β-strand | 188-190 | 3 | 3 |
| β-strand | 193-199 | 7 | 3 |
| α-helix | 211-214 | 4 | |
| β-strand | 219-225 | 7 | 3 |
| α-helix | 241-253 | 13 | |
| β-strand | 262-268 | 7 | 3 |
| α-helix | 270-276 | 7 | |
| α-helix | 298-308 | 11 | |
| β-strand | 318-322 | 5 | 3 |
| α-helix | 330-349 | 20 | |
Chain B: 2 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-24 | 21 | |
| β-strand | 47-51 | 5 | 4 |
| β-strand | 58-63 | 6 | 5 |
| β-strand | 69-74 | 6 | 5 |
| β-strand | 78-83 | 6 | 5 |
| β-strand | 89-94 | 6 | 5 |
| β-strand | 100-105 | 6 | 6 |
| β-strand | 111-116 | 6 | 6 |
| β-strand | 120-125 | 6 | 6 |
| β-strand | 135-140 | 6 | 6 |
| β-strand | 149-151 | 3 | 7 |
| β-strand | 156-160 | 5 | 7 |
| β-strand | 165-170 | 6 | 7 |
| β-strand | 176-181 | 6 | 7 |
| α-helix | 186-187 | 2 | |
| β-strand | 189-192 | 4 | 8 |
| β-strand | 198-202 | 5 | 8 |
| β-strand | 208-212 | 5 | 8 |
| β-strand | 220-222 | 3 | 8 |
| β-strand | 229-234 | 6 | 9 |
| β-strand | 240-245 | 6 | 9 |
| β-strand | 250-254 | 5 | 9 |
| β-strand | 259-263 | 5 | 9 |
| β-strand | 273-278 | 6 | 10 |
| β-strand | 284-289 | 6 | 10 |
| β-strand | 294-298 | 5 | 10 |
| β-strand | 304-308 | 5 | 10 |
| β-strand | 317-320 | 4 | 4 |
| β-strand | 327-331 | 5 | 4 |
| β-strand | 335-339 | 5 | 4 |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-23 | 16 | |
| α-helix | 30-45 | 16 | |
Chain H: 4 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 19-25 | 7 | 11 |
| α-helix | 29-31 | 3 | |
| β-strand | 35-39 | 5 | 12 |
| β-strand | 45-51 | 7 | 12 |
| α-helix | 53-55 | 3 | |
| β-strand | 58-60 | 3 | 12 |
| β-strand | 68-73 | 6 | 11 |
| β-strand | 78-83 | 6 | 11 |
| α-helix | 88-90 | 3 | |
| β-strand | 93-97 | 5 | 12 |
| β-strand | 111 | 1 | 12 |
| β-strand | 115-116 | 2 | 12 |
| β-strand | 146 | 1 | 13 |
| β-strand | 155-159 | 5 | 14 |
| β-strand | 166 | 1 | 15 |
| β-strand | 172 | 1 | 15 |
| β-strand | 174-179 | 6 | 13 |
| β-strand | 186-189 | 4 | 13 |
| β-strand | 195 | 1 | 13 |
| β-strand | 203-206 | 4 | 14 |
| β-strand | 212-216 | 5 | 14 |
| α-helix | 221-223 | 3 | |
| β-strand | 226-231 | 6 | 13 |
| β-strand | 243-244 | 2 | 13 |
Chain R: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-78 | 30 | |
| α-helix | 85-110 | 26 | |
| α-helix | 121-154 | 34 | |
| α-helix | 165-189 | 25 | |
| β-strand | 191-194 | 4 | 1 |
| β-strand | 200-203 | 4 | 1 |
| α-helix | 211-222 | 12 | |
| α-helix | 223-227 | 5 | |
| α-helix | 228-245 | 18 | |
| α-helix | 253-254 | 2 | |
| α-helix | 256-289 | 34 | |
| β-strand | 292 | 1 | 2 |
| β-strand | 295 | 1 | 2 |
| α-helix | 297-325 | 29 | |
| α-helix | 332-339 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| P2Y purinoceptor 1 | R | protein | 413 | Homo sapiens | P47900 (AlphaFold model) |
| Guanine nucleotide-binding protein G(11) subunit alpha | A | protein | 353 | Homo sapiens | P29992 (AlphaFold model), P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 346 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 71 | Homo sapiens | P59768 |
| scfv16 | H | protein | 247 | Homo sapiens | |
Sequence of entity 1 (R), FASTA
>7XXH_1 P2Y purinoceptor 1 (chains R)
GAPTEVLWPAVPNGTDAAFLAGPGSSWGNSTVASTAAVSSSFKCALTKTGFQFYYLPAVY
ILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWI
FGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLI
VVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYG
LIVRALIYKDLDNSPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAF
NDRVYATYQVTRGLASLNSCVDPILYFLAGDTFRRRLSRATRKASRRSEANLQSKSEDMT
LNILPEFKQNGDTSLEFLEVLFQGPGSWSHPQFEKGSGAGASAGSWSHPQFEK
Sequence of entity 2 (A), FASTA
>7XXH_2 Guanine nucleotide-binding protein G(11) subunit alpha (chains A)
MGCTLSAEDKAAVERSKMIDRNLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAG
YSEEDKRGFTKLVYQNIFTAMQAMIRAMETLKILYKYEQNKANALLIREVDVEKVTTFEH
QYVSAIKTLWEDPGIQECYDRRREYQLSDSAKYYLTDVDRIATLGYLPTQQDVLRVRVPT
TGIIEYPFDLENIIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNEN
RMEESKALFRTIITYPWFQNSSVILFLNKKDLLEDKILYSHLVDYFPEFDGPQRDAQAAR
EFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV
Sequence of entity 3 (B), FASTA
>7XXH_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGH
LAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVAC
GGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETG
QQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICF
FPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNC
NVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 4 (G), FASTA
>7XXH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 5 (H), FASTA
>7XXH_5 scfv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 6AD | 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate) | C11 H17 N5 O10 P2 S | 1 |
Primary citation
Structural insights into signal transduction of the purinergic receptors P2Y1R and P2Y12R. Li, B., Han, S., Wang, M. et al. Protein Cell (2023) 14:382-386. DOI 10.1093/procel/pwac025 · PubMed
Other PDB entries of the same protein (UniProt P47900 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4XNV 2.2 Å, The human P2Y1 receptor in complex with BPTU
- 4XNW 2.7 Å, The human P2Y1 receptor in complex with MRS2500
- 9JCL 2.76 Å, ADP-bound purinergic receptor 1 with L266P mutant in complex with miniGs/q
- 8WJX 3.2 Å, ADP-bound purinergic receptor 1 in complex with miniGs/q
Browse structure collections
About this viewer
MolViewer shows 7XXH 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.