7WF7: Sphingosine 1-phosphate receptor 1
Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to S1P. Determined by electron microscopy at 3.4 Å resolution. Released 5 Jan 2022.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 8,136
- Mol. weight
- 155.79 kDa
- Ligands
- S1P
- Released
- 5 Jan 2022
Explore 7WF7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7WF7 contains 30 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: 15 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-32 | 9 | |
| α-helix | 47-69 | 23 | |
| α-helix | 79-103 | 25 | |
| α-helix | 107-110 | 4 | |
| α-helix | 115-145 | 31 | |
| α-helix | 159-176 | 18 | |
| α-helix | 178-180 | 3 | |
| α-helix | 188-190 | 3 | |
| α-helix | 202-233 | 32 | |
| α-helix | 255-279 | 25 | |
| α-helix | 288-291 | 4 | |
| α-helix | 297-302 | 6 | |
| α-helix | 303-305 | 3 | |
| α-helix | 307-310 | 4 | |
| α-helix | 316-323 | 8 | |
Chain B: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-30 | 24 | |
| β-strand | 34-39 | 6 | 1 |
| α-helix | 46-52 | 7 | |
| β-strand | 185-191 | 7 | 1 |
| β-strand | 194-200 | 7 | 1 |
| α-helix | 211-214 | 4 | |
| β-strand | 220-223 | 4 | 1 |
| β-strand | 264-267 | 4 | 1 |
| β-strand | 319-322 | 4 | 1 |
| α-helix | 330-350 | 21 | |
Chain C: 5 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-23 | 19 | |
| α-helix | 30-33 | 4 | |
| α-helix | 34-36 | 3 | |
| α-helix | 38-39 | 2 | |
| β-strand | 47-51 | 5 | 2 |
| β-strand | 58-63 | 6 | 3 |
| β-strand | 69-74 | 6 | 3 |
| β-strand | 78-83 | 6 | 3 |
| β-strand | 88-94 | 7 | 3 |
| β-strand | 100-102 | 3 | 4 |
| β-strand | 105 | 1 | 4 |
| β-strand | 111-116 | 6 | 4 |
| β-strand | 120-125 | 6 | 4 |
| β-strand | 134-140 | 7 | 4 |
| α-helix | 145 | 1 | |
| β-strand | 146-151 | 6 | 5 |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 165-170 | 6 | 5 |
| β-strand | 176-180 | 5 | 5 |
| β-strand | 187-192 | 6 | 6 |
| β-strand | 199-203 | 5 | 6 |
| β-strand | 207-211 | 5 | 6 |
| β-strand | 221-223 | 3 | 6 |
| β-strand | 229-234 | 6 | 7 |
| β-strand | 240-245 | 6 | 7 |
| β-strand | 249-254 | 6 | 7 |
| β-strand | 260-265 | 6 | 7 |
| β-strand | 273-277 | 5 | 8 |
| β-strand | 284-289 | 6 | 8 |
| β-strand | 294-298 | 5 | 8 |
| β-strand | 305-307 | 3 | 8 |
| β-strand | 315-320 | 6 | 2 |
| β-strand | 327-331 | 5 | 2 |
| β-strand | 336-339 | 4 | 2 |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-23 | 13 | |
| α-helix | 30-43 | 14 | |
| α-helix | 56-58 | 3 | |
Chain E: 3 helices, 23 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 | 58-59 | 2 | 10 |
| 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 |
| β-strand | 128-130 | 3 | 11 |
| β-strand | 134-136 | 3 | 12 |
| β-strand | 143-149 | 7 | 11 |
| β-strand | 154 | 1 | 13 |
| β-strand | 160 | 1 | 13 |
| β-strand | 162-167 | 6 | 12 |
| β-strand | 174-178 | 5 | 12 |
| β-strand | 182-183 | 2 | 12 |
| α-helix | 184 | 1 | |
| β-strand | 191-196 | 6 | 11 |
| β-strand | 199-204 | 6 | 11 |
| β-strand | 214-219 | 6 | 12 |
| β-strand | 231-234 | 4 | 12 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Sphingosine 1-phosphate receptor 1 | A | protein | 382 | Homo sapiens | P21453 (AlphaFold model) |
| Guanine nucleotide-binding protein G(i) subunit alpha-1 | B | protein | 354 | Homo sapiens | P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | C | protein | 345 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | D | protein | 71 | Homo sapiens | P59768 (AlphaFold model) |
| scFv16 | E | protein | 247 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>7WF7_1 Sphingosine 1-phosphate receptor 1 (chains A)
MGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISADKENSIKLTSVVFILICCFII
LENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTYKLTPAQWFLR
EGSMFVALSASVWSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVISLILGGLPIM
GWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYCRIYSLVRTRSRRLTFRKN
ISKASRSSEKSLALLKTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDILFRAEYFLVLA
VLNSGTNPIIYTLTNKEMRRAFIRIMSCCKCPSGDSAGKFKRPIIAGMEFSRSKSDNSSH
PQKDEGDNPETIMSSGNVNSSS
Sequence of entity 2 (B), FASTA
>7WF7_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF
Sequence of entity 3 (C), FASTA
>7WF7_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 4 (D), FASTA
>7WF7_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 5 (E), FASTA
>7WF7_5 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| S1P | (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate | C18 H38 N O5 P | 1 |
Primary citation
Structural basis of sphingosine-1-phosphate receptor 1 activation and biased agonism. Xu, Z., Ikuta, T., Kawakami, K. et al. Nat Chem Biol (2022) 18:281-288. DOI 10.1038/s41589-021-00930-3 · PubMed
Other PDB entries of the same protein (UniProt P21453 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7TD4 2.6 Å, Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod
- 9VNZ 2.79 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with HY-X-1011
- 9VO0 2.79 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with Ponesimod
- 3V2Y 2.8 Å, Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A
- 7VIF 2.83 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with (S)-FTY720-P
- 7EO4 2.86 Å, Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to BAF312
- 7VIE 2.86 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with S1P
- 7EO2 2.89 Å, Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to FTY720p
- 7VIG 2.89 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307
- 9VO1 2.97 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with SAR247799
- 7EVY 2.98 Å, Cryo-EM structure of siponimod -bound Sphingosine-1-phosphate receptor 1 in complex with…
- 7VIH 2.98 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307
Browse structure collections
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