9KVG: PDB entry 9KVG

A Cryo_EM structure of 5_HT1A complex with 5-Meo-DMT. Determined by electron microscopy at 2.63 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 2.63 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,935
Mol. weight: 158.15 kDa
Ligands: J40, Y01, CHO, YFW
Released: 3 Dec 2025

Explore 9KVG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KVG contains 44 α-helices and 58 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: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	1
α-helix	46-53	8
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	227-230	4
α-helix	236-238	3
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	330-351	22

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	17-29	13
α-helix	35-38	4
α-helix	39-41	3
α-helix	43-44	2
β-strand	52-56	5	2
β-strand	63-68	6	3
β-strand	74-79	6	3
β-strand	83-88	6	3
β-strand	93-99	7	3
β-strand	105-110	6	4
β-strand	116-121	6	4
β-strand	126-130	5	4
β-strand	139-144	6	4
β-strand	151-156	6	5
β-strand	161-166	6	5
β-strand	171-175	5	5
β-strand	180-185	6	5
α-helix	191	1
β-strand	192-197	6	6
β-strand	203-208	6	6
β-strand	212-217	6	6
β-strand	223-227	5	6
β-strand	234-239	6	7
β-strand	245-250	6	7
β-strand	255-259	5	7
β-strand	265-269	5	7
β-strand	278-283	6	8
β-strand	289-294	6	8
β-strand	299-303	5	8
β-strand	309-313	5	8
β-strand	320-325	6	2
β-strand	332-336	5	2
β-strand	341-344	4	2

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	9-11	3	10
β-strand	17-24	8	9
β-strand	32-38	7	10
β-strand	44-50	7	10
α-helix	52-54	3
β-strand	57-59	3	10
β-strand	64	1	9
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	87-89	3
β-strand	91-98	8	10
β-strand	110	1	10
β-strand	114-118	5	10
α-helix	137-139	3
β-strand	140-142	3	11
β-strand	146-148	3	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	186-189	4	12
β-strand	195	1	12
α-helix	196	1
β-strand	203-207	5	11
β-strand	211-216	6	11
α-helix	221-223	3
β-strand	225-231	7	12
β-strand	243-246	4	12

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	10-18	9
α-helix	20-23	4
α-helix	29-42	14
α-helix	44-46	3
α-helix	52-54	3
α-helix	55-57	3

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	35-63	29
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-98	9
α-helix	106-139	34
α-helix	141-142	2
α-helix	143-147	5
α-helix	150-168	19
α-helix	170-173	4
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-227	22
α-helix	326-370	45
α-helix	379-397	19
α-helix	398-402	5
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	344	Homo sapiens	P62873 (AlphaFold model)
SCFV16	E	protein	247	Homo sapiens
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	398	Homo sapiens	P08908 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KVG_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLADEAEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9KVG_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>9KVG_3 SCFV16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 4 (G), FASTA

>9KVG_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>9KVG_5 5-hydroxytryptamine receptor 1A (chains R)
TTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLM
VSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCCTSSIWHLCAIALDRYWAITDPIDY
VNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPEDRSDPDACTISKDHGYTIYSTFGAF
YIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWR
LGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERK
NERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCESSCHMPTLLGAI
INWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ

Ligands and cofactors

ID	Name	Formula	Copies
J40	[(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cycl…	C39 H68 O16 P2	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1
CHO	Glycochenodeoxycholic acid	C26 H43 N O5	1
YFW	2-(5-methoxy-1H-indol-3-yl)-N,N-dimethylethan-1-amine	C13 H18 N2 O	1

Primary citation

Structural Pharmacology of Bufotenine Derivatives in Activating the 5-HT 1A Receptor for Therapeutic Potential in Depression and Anxiety. Li, S.J., Yuan, Q.N., Wu, W.Y. et al. Research (Wash D C) (2025) 8:0987-0987. DOI 10.34133/research.0987 · 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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