9MD1: PDB entry 9MD1

Buspirone-bound serotonin 1A (5-HT1A) receptor-Gz protein complex. Determined by electron microscopy at 3.03 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 5
Atoms: 8,507
Mol. weight: 217.23 kDa
Ligands: J40, CLR, YLX
Released: 13 Aug 2025

Explore 9MD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MD1 contains 42 α-helices and 34 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-38	6	1
β-strand	186-191	6	1
β-strand	196-201	6	1
β-strand	221-226	6	1
β-strand	264-269	6	1
β-strand	320-324	5	1
α-helix	331-351	21

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	16-25	10
α-helix	30-33	4
α-helix	38-39	2
β-strand	49-52	4	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	102-105	4	4
β-strand	111-115	5	4
β-strand	121-125	5	4
β-strand	135-139	5	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-181	7	5
β-strand	189-192	4	6
β-strand	198-202	5	6
β-strand	208-212	5	6
β-strand	218-222	5	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	304-307	4	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-338	4	2

Chain C: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	36-63	28
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-99	10
α-helix	106-139	34
α-helix	141-142	2
α-helix	143-147	5
α-helix	150-166	17
α-helix	170-172	3
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-227	22
α-helix	331-367	37
α-helix	368-370	3
α-helix	379-390	12
α-helix	392-400	9
α-helix	405-414	10

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	20-24	5
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	36-62	27
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-99	10
α-helix	106-139	34
α-helix	141-146	6
α-helix	150-167	18
α-helix	193-200	8
α-helix	201-205	5
α-helix	206-227	22
α-helix	331-337	7
α-helix	345-367	23
α-helix	368-370	3
α-helix	379-390	12
α-helix	392-400	9
α-helix	405-414	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(z) subunit alpha	A	protein	355	Homo sapiens	P19086 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	358	Homo sapiens	P62873 (AlphaFold model)
Soluble cytochrome b562,5-hydroxytryptamine receptor 1A	C, R	protein	552	Escherichia coli, Homo sapiens	P08908 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	80	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9MD1_1 Guanine nucleotide-binding protein G(z) subunit alpha (chains A)
MGCRQSSEEKEAARRSRRIDRHLRSESQRQRREIKLLLLGTSNSGKSTIVKQMKIIHSGG
FNLEACKEYKPLIIYNAIDSLTRIIRALAALRIDFHNPDRAYDAVQLFALTGPAESKGEI
TPELLGVMRRLWADPGAQACFSRSSEYHLEDNAAYYLNDLERIAAADYIPTVEDILRSRD
MTTGIVENKFTFKELTFKMVDVGGQRSERKKWIHCFEGVTAIIFCVELSGYDLKLYEDNQ
TSRMAESLRLFDSICNNNWFINTSLILFLNKKDLLAEKIRRIPLTICFPEYKGQNTYEEA
AVYIQRQFEDLNRNKETKEIYSHFTCATDTSNIQFVFDAVTDVIIQNNLKYIGLC

Sequence of entity 2 (B), FASTA

>9MD1_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C, R), FASTA

>9MD1_3 Soluble cytochrome b562,5-hydroxytryptamine receptor 1A (chains C, R)
MKTIIALSYIFCLVFADYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTADLEDNWETLN
DNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQ
IDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLTGISDVTVSYQVITSLLLGTLIFCA
VLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCD
LFIALDVLCCTSSIWHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIP
PMLGWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTV
KKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAAL
EVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGII
MGTFILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNA
FKKIIKCKFCRQ

Sequence of entity 4 (G), FASTA

>9MD1_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
J40	[(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cycl…	C39 H68 O16 P2	2
CLR	Cholesterol	C27 H46 O	8
YLX	Buspirone	C21 H31 N5 O2	2

Primary citation

Structural determinants of G protein subtype selectivity at the serotonin receptor 5-HT1A. Warren, A.L., Zilberg, G., Abbassi, A. et al. Sci Adv (2025) 11:eadu9851-eadu9851. DOI 10.1126/sciadv.adu9851 · PubMed

Other PDB entries of the same protein (UniProt P19086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DZS 2.65 Å, GR89,696 bound Kappa Opioid Receptor in complex with Gz
9WSW 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-Gz-scFv16 complex

Browse structure collections

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