7SR8: PDB entry 7SR8
Molecular mechanism of the the wake-promoting agent TAK-925. Determined by electron microscopy at 3.3 Å resolution. Released 8 Jun 2022.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 9,083
- Mol. weight
- 150.38 kDa
- Ligands
- OLA, A6F
- Released
- 8 Jun 2022
Explore 7SR8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7SR8 contains 32 α-helices and 66 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 | 7-31 | 25 | |
| β-strand | 34-40 | 7 | 1 |
| β-strand | 62-68 | 7 | 1 |
| β-strand | 71-77 | 7 | 1 |
| β-strand | 97-103 | 7 | 1 |
| α-helix | 110-122 | 13 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-136 | 7 | 1 |
| α-helix | 138-147 | 10 | |
| α-helix | 152-154 | 3 | |
| α-helix | 157-159 | 3 | |
| α-helix | 176-195 | 20 | |
| β-strand | 203-204 | 2 | 1 |
| β-strand | 207 | 1 | 1 |
| α-helix | 216-234 | 19 | |
Chain B: 4 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-25 | 23 | |
| 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 | 100-105 | 6 | 4 |
| β-strand | 111-116 | 6 | 4 |
| β-strand | 120-125 | 6 | 4 |
| β-strand | 134-140 | 7 | 4 |
| β-strand | 146-152 | 7 | 5 |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 165-170 | 6 | 5 |
| β-strand | 176-181 | 6 | 5 |
| β-strand | 187 | 1 | 6 |
| β-strand | 191-192 | 2 | 7 |
| β-strand | 198-202 | 5 | 7 |
| β-strand | 203 | 1 | 6 |
| 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 | 9 |
| β-strand | 284-289 | 6 | 9 |
| β-strand | 293-298 | 6 | 9 |
| β-strand | 304-309 | 6 | 9 |
| β-strand | 315 | 1 | 10 |
| β-strand | 320 | 1 | 2 |
| β-strand | 327-329 | 3 | 2 |
| β-strand | 331 | 1 | 10 |
| β-strand | 336-339 | 4 | 2 |
Chain E: 6 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 10-12 | 3 | 12 |
| β-strand | 17-25 | 9 | 11 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-40 | 8 | 12 |
| β-strand | 44-51 | 8 | 12 |
| β-strand | 58-60 | 3 | 12 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 11 |
| β-strand | 78-84 | 7 | 11 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 12 |
| β-strand | 111 | 1 | 12 |
| β-strand | 115-119 | 5 | 12 |
| β-strand | 140-142 | 3 | 13 |
| β-strand | 146-149 | 4 | 14 |
| β-strand | 155-161 | 7 | 13 |
| β-strand | 166 | 1 | 15 |
| β-strand | 172 | 1 | 15 |
| β-strand | 174-179 | 6 | 14 |
| β-strand | 186-190 | 5 | 14 |
| β-strand | 194-195 | 2 | 14 |
| α-helix | 196 | 1 | |
| β-strand | 203-208 | 6 | 13 |
| β-strand | 211-216 | 6 | 13 |
| α-helix | 221-223 | 3 | |
| β-strand | 226-231 | 6 | 14 |
| α-helix | 237 | 1 | |
| β-strand | 238-239 | 2 | 14 |
| β-strand | 243-247 | 5 | 14 |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-23 | 18 | |
| α-helix | 30-44 | 15 | |
Chain R: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 54-81 | 28 | |
| α-helix | 88-116 | 29 | |
| β-strand | 119 | 1 | 16 |
| α-helix | 124-157 | 34 | |
| α-helix | 166-183 | 18 | |
| α-helix | 185-189 | 5 | |
| β-strand | 192-196 | 5 | 16 |
| β-strand | 207-211 | 5 | 16 |
| α-helix | 219-228 | 10 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-251 | 18 | |
| α-helix | 294-328 | 35 | |
| α-helix | 339-361 | 23 | |
| α-helix | 362-366 | 5 | |
| α-helix | 369-379 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| a modified Guanine nucleotide-binding protein G(q) subunit alpha | A | protein | 238 | Homo sapiens | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 340 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 82 | Homo sapiens | P59768 (AlphaFold model) |
| scFv16 | E | protein | 259 | Homo sapiens | |
| Hypocretin receptor type 2 | R | protein | 407 | Homo sapiens | O43614 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>7SR8_1 a modified Guanine nucleotide-binding protein G(q) subunit alpha (chains A)
MGSTLSAEDKAAVERSKMIDRNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHTSG
IFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSI
WNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTR
AKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLREYNLV
Sequence of entity 2 (B), FASTA
>7SR8_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 3 (G), FASTA
>7SR8_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MGHHHHHHHHGGASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDP
LLTPVPASENPFREKKFFCAIL
Sequence of entity 4 (E), FASTA
>7SR8_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH
Sequence of entity 5 (R), FASTA
>7SR8_5 Hypocretin receptor type 2 (chains R)
MGTKLEDSPPCRNWSSASELNETQEPFLNPTDYDDEEFLRYLWREYLHPKEYEWVLIAGY
IIVFVVALIGNVLVCVAVWKNHHMRTVTNYFIVNLSLADVLVTITCLPATLVVDITETWF
FGQSLCKVIPYLQTVSVSVSVLTLSCIALDRWYAICHPLMFKSTAKRARNSIVIIWIVSC
IIMIPQAIVMECSTVFPGLANKTTLFTVCDERWGGEIYPKMYHICFFLVTYMAPLCLMVL
AYLQIFRKLWCRQIPGTSSVVQRKWKPLQPVSQPRGPGQPTKSRMSAVAAEIKQIRARRK
TARMLMVVLLVFAICYLPISILNVLKRVFGMFAHTEDRETVYAWFTFSHWLVYANSAANP
IIYNFLSGKFREEFKAAFSCCCLGVHHRQEDRLTRGRTSTESRKSLT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| OLA | Oleic acid | C18 H34 O2 | 4 |
| A6F | methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}m… | C21 H32 N2 O5 S | 1 |
Primary citation
Molecular mechanism of the wake-promoting agent TAK-925. Yin, J., Kang, Y., McGrath, A.P. et al. Nat Commun (2022) 13:2902-2902. DOI 10.1038/s41467-022-30601-3 · 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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