8FYT: PDB entry 8FYT

LSD-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex. Determined by electron microscopy at 2.64 Å resolution. Released 15 May 2024.

Method: Electron microscopy
Resolution: 2.64 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,321
Mol. weight: 151.87 kDa
Ligands: Y01, J40, 7LD
Released: 15 May 2024

Explore 8FYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FYT contains 34 α-helices and 36 β-strands across 4 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	1
α-helix	46-53	8
α-helix	178-180	3
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	330-351	22

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
α-helix	38-39	2
β-strand	49-51	3	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-150	5	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	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
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-307	4	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-338	3	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	30-43	14
α-helix	53-55	3

Chain R: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	37-63	27
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-99	10
α-helix	106-139	34
α-helix	141-145	5
α-helix	150-168	19
α-helix	170-172	3
α-helix	179-182	4
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-227	22
α-helix	325-367	43
α-helix	379-400	22
α-helix	405-414	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,5-hydroxytryptamine receptor 1A,5-hydroxytryptamine receptor 1A	R	protein	552	Homo sapiens	P08908 (AlphaFold model), P0ABE7 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (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	80	Homo sapiens	P59768

Sequence of entity 1 (R), FASTA

>8FYT_1 Soluble cytochrome b562,5-hydroxytryptamine receptor 1A,5-hydroxytryptamine receptor 1A (chains R)
MKTIIALSYIFCLVFADYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTADLEDNWETLN
DNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQ
IDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLTGISDVTVSYQVITSLLLGTLIFCA
VLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCD
LFIALDVLCCTSSIWHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIP
PMLGWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTV
KKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAAL
EVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGII
MGTFILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNA
FKKIIKCKFCRQ

Sequence of entity 2 (A), FASTA

>8FYT_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>8FYT_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>8FYT_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSA

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	2
J40	[(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cycl…	C39 H68 O16 P2	1
7LD	(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide	C20 H25 N3 O	1

Primary citation

Structural pharmacology and therapeutic potential of 5-methoxytryptamines. Warren, A.L., Lankri, D., Cunningham, M.J. et al. Nature (2024) 630:237-246. DOI 10.1038/s41586-024-07403-2 · PubMed

Other PDB entries of the same protein (UniProt P08908 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
8PJK 2.4 Å, ST171-bound serotonin 5-HT1A receptor - Gi Protein Complex
9VJE 2.47 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with buspirone
9KVI 2.54 Å, A Cryo_EM structure of 5_HT1A complex with DMT
9KVH 2.59 Å, A Cryo_EM structure of 5_HT1A complex with TMT
8FYX 2.62 Å, Buspirone-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex
9VJ6 2.62 Å, Cryo-EM structure of 5-HT1AR-Gi3 in complex with F-15599
9KVG 2.63 Å, A Cryo_EM structure of 5_HT1A complex with 5-Meo-DMT
9VJG 2.67 Å, Cryo-EM structure of 5-HT1AR-Gz in complex with (R)-8-OH-DPAT
9VJ5 2.69 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
9VJF 2.7 Å, Cryo-EM structure of 5-HT1AR-Gi3 in complex with buspirone
9DYF 2.74 Å, Asenapine-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex

Browse structure collections

About this viewer

MolViewer shows 8FYT 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.