7F9Y: Ghrelin-bound ghrelin receptor
ghrelin-bound ghrelin receptor in complex with Gq. Determined by electron microscopy at 2.9 Å resolution. Released 18 Aug 2021.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Homo sapiens, Lama glama
- Chains
- 6
- Atoms
- 8,354
- Mol. weight
- 183.74 kDa
- Ligands
- OCA, CLR
- Released
- 18 Aug 2021
Explore 7F9Y in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7F9Y contains 40 α-helices and 47 β-strands across 6 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: 12 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-39 | 23 | |
| β-strand | 41-47 | 7 | 1 |
| α-helix | 53-59 | 7 | |
| β-strand | 207-214 | 8 | 1 |
| β-strand | 217-224 | 8 | 1 |
| α-helix | 231-234 | 4 | |
| α-helix | 235-237 | 3 | |
| β-strand | 243-249 | 7 | 1 |
| α-helix | 266-278 | 13 | |
| α-helix | 280-282 | 3 | |
| β-strand | 286-292 | 7 | 1 |
| α-helix | 294-302 | 9 | |
| α-helix | 308-311 | 4 | |
| α-helix | 313-317 | 5 | |
| α-helix | 326-327 | 2 | |
| α-helix | 332-351 | 20 | |
| β-strand | 359-363 | 5 | 1 |
| α-helix | 371-390 | 20 | |
Chain B: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-25 | 22 | |
| 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 | 146-153 | 8 | 5 |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 166-170 | 5 | 5 |
| β-strand | 175-180 | 6 | 5 |
| β-strand | 189-192 | 4 | 6 |
| β-strand | 198-202 | 5 | 6 |
| β-strand | 207-212 | 6 | 6 |
| β-strand | 218-223 | 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 | 273-278 | 6 | 8 |
| β-strand | 284-289 | 6 | 8 |
| β-strand | 294-298 | 5 | 8 |
| β-strand | 304-308 | 5 | 8 |
| β-strand | 315-320 | 6 | 2 |
| β-strand | 327-331 | 5 | 2 |
| β-strand | 336-339 | 4 | 2 |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-11 | 4 | |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-23 | 17 | |
| α-helix | 30-43 | 14 | |
| α-helix | 45-47 | 3 | |
| α-helix | 53-55 | 3 | |
Chain N: 3 helices, 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 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 9 |
| β-strand | 78-84 | 7 | 9 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 10 |
| β-strand | 118 | 1 | 10 |
| β-strand | 122-126 | 5 | 10 |
Chain R: 16 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-69 | 30 | |
| α-helix | 77-94 | 18 | |
| α-helix | 96-104 | 9 | |
| α-helix | 113-146 | 34 | |
| α-helix | 148-151 | 4 | |
| α-helix | 157-175 | 19 | |
| α-helix | 178-181 | 4 | |
| β-strand | 182-185 | 4 | 11 |
| α-helix | 192-194 | 3 | |
| β-strand | 197-200 | 4 | 11 |
| α-helix | 202-206 | 5 | |
| α-helix | 210 | 1 | |
| α-helix | 211-215 | 5 | |
| α-helix | 216-218 | 3 | |
| α-helix | 222-240 | 19 | |
| α-helix | 258-288 | 31 | |
| α-helix | 297-322 | 26 | |
| α-helix | 328-333 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Engineered G-alpha-q subunit | A | protein | 362 | Homo sapiens | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 371 | Homo sapiens | P62873 (AlphaFold model) |
| Ghrelin-28 | C | protein | 28 | Homo sapiens | Q9UBU3 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 71 | Homo sapiens | P59768 (AlphaFold model) |
| NB35 | N | protein | 140 | Lama glama | |
| Soluble cytochrome b562 | R | protein | 661 | Homo sapiens | P0ABE7 (AlphaFold model), Q92847 |
Sequence of entity 1 (A), FASTA
>7F9Y_1 Engineered G-alpha-q subunit (chains A)
MMGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVN
GYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFM
TAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRV
KTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALND
FKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDP
RVTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYN
LV
Sequence of entity 2 (B), FASTA
>7F9Y_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSG
VSGWRLFKKIS
Sequence of entity 3 (C), FASTA
>7F9Y_3 Ghrelin-28 (chains C)
GSSFLSPEHQRVQQRKESKKPPAKLQPR
Sequence of entity 4 (G), FASTA
>7F9Y_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 5 (N), FASTA
>7F9Y_5 NB35 (chains N)
MAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASI
SYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYR
GQGTQVTVSSHHHHHHEPEA
Sequence of entity 6 (R), FASTA
>7F9Y_6 Soluble cytochrome b562 (chains R)
MKTIIALSYIFCLVFAHHHHHHHHHHADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR
AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL
KTTRNAYIQKYLMWNATPSEEPGFNLTLADLDWDASPGNDSLGDELLQLFPAPLLAGVTA
TCVALFVVGIAGNLLTMLVVSRFRELRTTTNLYLSSMAFSDLLIFLCMPLDLVRLWQYRP
WNFGDLLCKLFQFVSESCTYATVLTITALSVERYFAICFPLRAKVVVTKGRVKLVIFVIW
AVAFCSAGPIFVLVGVEHENGTDPWDTNECRPTEFAVRSGLLTVMVWVSSIFFFLPVFCL
TVLYSLIGRKLWRRRRGDAVVGASLRDQNHKQTVKMLAVVVFAFILCWLPFHVGRYLFSK
SFEPGSLEIAQISQYCNLVSFVLFYLSAAINPILYNIMSKKYRVAVFRLLGFEPFSQRKL
STLKDESSRAWTESSINTGSAGSVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAV
SVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGT
LVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTIN
S
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| OCA | Octanoic acid (caprylic acid) | C8 H16 O2 | 1 |
| CLR | Cholesterol | C27 H46 O | 2 |
Primary citation
Molecular recognition of an acyl-peptide hormone and activation of ghrelin receptor. Wang, Y., Guo, S., Zhuang, Y. et al. Nat Commun (2021) 12:5064-5064. DOI 10.1038/s41467-021-25364-2 · 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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