9AS6: Global reconstruction of 5-HT2AR

Global reconstruction of 5-HT2AR bound to mescaline in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM). Determined by electron microscopy at 3.07 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,268
Mol. weight: 156.89 kDa
Ligands: A1AFW
Released: 2 Apr 2025

Explore 9AS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AS6 contains 34 α-helices and 63 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: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	81-100	20
α-helix	108-126	19
α-helix	128-136	9
α-helix	145-178	34
α-helix	180-184	5
α-helix	189-206	18
α-helix	209-216	8
α-helix	218-220	3
β-strand	222-223	2	8
β-strand	226-227	2	8
α-helix	232-240	9
α-helix	245-261	17
α-helix	316-348	33
α-helix	355-370	16
α-helix	371-374	4
α-helix	376-382	7
α-helix	385-394	10

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	9
β-strand	70-76	7	9
β-strand	79-85	7	9
α-helix	96-98	3
β-strand	105-111	7	9
α-helix	118-129	12
α-helix	133-135	3
β-strand	138-144	7	9
α-helix	146-155	10
α-helix	160-163	4
α-helix	165-169	5
α-helix	184-204	21
β-strand	211-215	5	9
α-helix	224-242	19

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	30-33	4
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	89-94	6	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	166-170	5	4
β-strand	175-180	6	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	208-212	5	5
β-strand	218-222	5	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	249-254	6	6
β-strand	259-265	7	6
α-helix	272	1
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	317-320	4	1
β-strand	327-330	4	1
β-strand	336-339	4	1

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	53-55	3

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-11	2	11
β-strand	18-25	8	10
β-strand	33-34	2	12
β-strand	38-39	2	11
β-strand	45-46	2	11
β-strand	49-51	3	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-94	3	11
β-strand	97-99	3	12
β-strand	110-111	2	12
β-strand	115-118	4	11
β-strand	128-130	3	13
β-strand	134-136	3	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
α-helix	184	1
β-strand	192-196	5	13
β-strand	199-204	6	13
β-strand	214-219	6	14
α-helix	225	1
β-strand	227	1	14
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
5-hydroxytryptamine receptor 2A	A	protein	471	Homo sapiens	P28223 (AlphaFold model)
G subunit q (Gi2-mini-Gq chimeric)	B	protein	246	Homo sapiens
single chain Fab (svFv16)	E	protein	267	Homo sapiens

Sequence of entity 1 (C), FASTA

>9AS6_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (D), FASTA

>9AS6_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (A), FASTA

>9AS6_3 5-hydroxytryptamine receptor 2A (chains A)
MDILCEENTSLSSTTNSLMQLNDDTRLYSNDFNSGEANTSDAFNWTVDSENRTNLSCEGC
LSPSCLSLLHLQEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIAD
MLLGFLVMPVSMLTILYGYRWPLPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNP
IHHSRFNSRTKAFLKIIAVWTISVGISMPIPVFGLQDDSKVFKEGSCLLADDNFVLIGSF
VSFFIPLTIMVITYFLTIKSLQKEATLCVSDLGTRAKLASFSFLPQSSLSSEKLFQRSIH
REPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNEDVIGA
LLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENKKPLQLILVNTIPALAYK
SSQLQMGQKKNSKQDAKTTDNDCSMVALGKQHSEEASKDNSDGVNEKVSCV

Sequence of entity 4 (B), FASTA

>9AS6_4 G subunit q (Gi2-mini-Gq chimeric) (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 5 (E), FASTA

>9AS6_5 single chain Fab (svFv16) (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1AFW	Mescaline	C11 H17 N O3	1

Primary citation

The structural diversity of psychedelic drug actions revealed. Gumpper, R.H., Jain, M.K., Kim, K. et al. Nat Commun (2025) 16:2734-2734. DOI 10.1038/s41467-025-57956-7 · 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

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