7EPT: PDB entry 7EPT
Structural basis for the tethered peptide activation of adhesion GPCRs. Determined by electron microscopy at 3.0 Å resolution. Released 11 May 2022.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 5
- Atoms
- 7,847
- Mol. weight
- 138.32 kDa
- Ligands
- PLM
- Released
- 11 May 2022
Explore 7EPT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7EPT contains 34 α-helices and 46 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 | 13-39 | 27 | |
| β-strand | 40-47 | 8 | 1 |
| β-strand | 208-214 | 7 | 1 |
| β-strand | 217-223 | 7 | 1 |
| α-helix | 234-236 | 3 | |
| β-strand | 243-248 | 6 | 1 |
| α-helix | 265-278 | 14 | |
| β-strand | 286-291 | 6 | 1 |
| α-helix | 296-303 | 8 | |
| α-helix | 308-311 | 4 | |
| α-helix | 313-317 | 5 | |
| α-helix | 332-349 | 18 | |
| β-strand | 359-360 | 2 | 1 |
| β-strand | 363 | 1 | 1 |
| α-helix | 371-390 | 20 | |
Chain B: 3 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-25 | 24 | |
| α-helix | 30-33 | 4 | |
| 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 |
| α-helix | 95 | 1 | |
| β-strand | 100-105 | 6 | 4 |
| β-strand | 111-116 | 6 | 4 |
| β-strand | 121-125 | 5 | 4 |
| β-strand | 134-139 | 6 | 4 |
| β-strand | 146-151 | 6 | 5 |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 165-170 | 6 | 5 |
| β-strand | 175-180 | 6 | 5 |
| β-strand | 187-192 | 6 | 6 |
| β-strand | 198-203 | 6 | 6 |
| β-strand | 208-212 | 5 | 6 |
| β-strand | 217-222 | 6 | 6 |
| β-strand | 229-234 | 6 | 7 |
| β-strand | 240-245 | 6 | 7 |
| β-strand | 250-254 | 5 | 7 |
| β-strand | 259-264 | 6 | 7 |
| β-strand | 276-278 | 3 | 8 |
| β-strand | 284-288 | 5 | 8 |
| β-strand | 293-298 | 6 | 8 |
| β-strand | 304-309 | 6 | 8 |
| β-strand | 315-320 | 6 | 2 |
| β-strand | 327-331 | 5 | 2 |
| β-strand | 336-339 | 4 | 2 |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-23 | 18 | |
| α-helix | 30-44 | 15 | |
| α-helix | 45-47 | 3 | |
Chain N: 1 helix, 11 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 | 34-39 | 6 | 10 |
| β-strand | 45-51 | 7 | 10 |
| β-strand | 58-60 | 3 | 10 |
| β-strand | 68-73 | 6 | 9 |
| β-strand | 78-84 | 7 | 9 |
| β-strand | 92-95 | 4 | 10 |
| β-strand | 98 | 1 | 10 |
| β-strand | 122-126 | 5 | 10 |
Chain R: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 547-551 | 5 | |
| α-helix | 558-559 | 2 | |
| α-helix | 562-591 | 30 | |
| α-helix | 596-598 | 3 | |
| α-helix | 601-622 | 22 | |
| α-helix | 630-657 | 28 | |
| α-helix | 658-662 | 5 | |
| α-helix | 672-676 | 5 | |
| α-helix | 677-681 | 5 | |
| α-helix | 682-690 | 9 | |
| α-helix | 696-699 | 4 | |
| α-helix | 714-740 | 27 | |
| α-helix | 756-769 | 14 | |
| α-helix | 771-773 | 3 | |
| α-helix | 774-777 | 4 | |
| α-helix | 785-795 | 11 | |
| α-helix | 798-803 | 6 | |
| α-helix | 804-808 | 5 | |
| α-helix | 811-825 | 15 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | A | protein | 394 | Homo sapiens | P63092 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 358 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 71 | Homo sapiens | P59768 (AlphaFold model) |
| Nanobody-35 | N | protein | 128 | synthetic construct | |
| Adhesion G-protein coupled receptor D1 | R | protein | 283 | Homo sapiens | Q6QNK2 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>7EPT_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQDDYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL
Sequence of entity 2 (B), FASTA
>7EPT_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 3 (G), FASTA
>7EPT_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 4 (N), FASTA
>7EPT_4 Nanobody-35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS
Sequence of entity 5 (R), FASTA
>7EPT_5 Adhesion G-protein coupled receptor D1 (chains R)
TNFAILMQVVPLELARGHQVALSSISYVGCSLSVLCLVATLVTFAVLSSVSTIRNQRYHI
HANLSFAVLVAQVLLLISFRLEPGTTPCQVMAVLLHYFFLSAFAWMLVEGLHLYSMVIKV
FGSEDSKHRYYYGMGWGFPLLICIISLSFAMDSYGTSNNCWLSLASGAIWAFVAPALFVI
VVNIGILIAVTRVISQISADNYKIHGDPSAFKLTAKAVAVLLPILGTSWVFGVLAVNGCA
VVFQYMFATLNSLQGLFIFLFHCLLNSEVRAAFKHKTKVWSLT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLM | Palmitic acid | C16 H32 O2 | 1 |
Primary citation
Structural basis for the tethered peptide activation of adhesion GPCRs. Ping, Y.Q., Xiao, P., Yang, F. et al. Nature (2022) 604:763-770. DOI 10.1038/s41586-022-04619-y · PubMed
Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
- 6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
- 8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
- 7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
- 7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
- 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
- 7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)
Browse structure collections
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