8PKM: PDB entry 8PKM

Befiradol-bound serotonin 5-HT1A receptor - Gi Protein Complex. Determined by electron microscopy at 2.9 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,929
Mol. weight: 140.25 kDa
Ligands: ZKV, T7M, CLR
Released: 29 May 2024

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

Secondary structure: helices and β-sheets

8PKM contains 30 α-helices and 37 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-38	5	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-222	3	1
β-strand	224-226	3	2
α-helix	227-230	4
α-helix	242-254	13
β-strand	263-264	2	1
β-strand	267-269	3	2
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-309	14
β-strand	319	1	1
β-strand	322-323	2	2
α-helix	331-350	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
α-helix	30-34	5
α-helix	38-42	5
β-strand	47-52	6	3
β-strand	58-63	6	4
β-strand	70-74	5	4
β-strand	78-81	4	4
β-strand	91-94	4	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	135-139	5	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	217-222	6	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	285-289	5	9
β-strand	294-296	3	9
β-strand	307	1	9
α-helix	308-310	3
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
α-helix	30-45	16

Chain R: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	35-62	28
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-98	9
α-helix	107-139	33
α-helix	141-145	5
α-helix	150-173	24
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-228	23
α-helix	329-367	39
α-helix	379-400	22
α-helix	405-414	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	352	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)
5-hydroxytryptamine receptor 1A	R	protein	466	Homo sapiens	P08908 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PKM_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8PKM_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTR
RTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPS
GNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCAL
WDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESD
INAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAG
YDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8PKM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8PKM_4 5-hydroxytryptamine receptor 1A (chains R)
MKTIIALSYIFCLVFADYKDDDDAAAAHHHHHHHHHHENLYFQGMDVLSPGQGNNTTSPP
APFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIG
SLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCCTSSIWHLCAIALDRYW
AITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPEDRSDPDACTISKDHGYT
IYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKSVNG
ESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPC
APASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCESSCH
MPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ

Ligands and cofactors

ID	Name	Formula	Copies
ZKV	(3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methyla…	C20 H22 Cl F2 N3 O	1
T7M	(2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahyd…	C46 H82 O16 P2	1
CLR	Cholesterol	C27 H46 O	1

Primary citation

Discovery of a functionally selective serotonin receptor (5-HT 1A R) agonist for the treatment of pain. Ullrich, A., Schneider, J., Braz, J.M. et al. Sci Adv (2025) 11:eadv9267-eadv9267. DOI 10.1126/sciadv.adv9267 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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