8X9S: PDB entry 8X9S

Identification, structure and agonist design of an androgen membrane receptor. Determined by electron microscopy at 3.49 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 3.49 Å
Organisms: Rattus norvegicus, Bos taurus, Homo sapiens
Chains: 4
Atoms: 6,774
Mol. weight: 153.5 kDa
Ligands: DHT
Released: 12 Feb 2025

Explore 8X9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X9S contains 30 α-helices and 35 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	17-38	22
β-strand	40-45	6	8
α-helix	54-58	5
β-strand	207-210	4	8
β-strand	213-214	2	8
β-strand	217-224	8	8
α-helix	235-237	3
β-strand	243-246	4	8
α-helix	267-277	11
β-strand	286-289	4	8
α-helix	294-301	8
α-helix	308-311	4
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-349	18
β-strand	359-361	3	8
α-helix	371-390	20

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-32	3
α-helix	38-39	2
β-strand	47-50	4	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	135-139	5	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	166-170	5	4
α-helix	172-174	3
β-strand	176-180	5	4
α-helix	186	1
β-strand	187-191	5	5
β-strand	198-203	6	5
β-strand	208-212	5	5
β-strand	218-220	3	5
β-strand	229-232	4	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	260-264	5	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	307	1	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	335-339	5	1

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-22	17
α-helix	30-43	14
α-helix	56-58	3

Chain R: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	567-590	24
α-helix	600-623	24
α-helix	630-661	32
α-helix	672-679	8
α-helix	682-693	12
α-helix	714-742	29
α-helix	754-769	16
α-helix	775-780	6
α-helix	788-794	7
α-helix	798-806	9
α-helix	811-826	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	344	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
Adhesion G-protein coupled receptor D1	R	protein	598	Homo sapiens	Q6QNK2 (AlphaFold model)
Gs protein alpha subunit	A	protein	361	Bos taurus	P04896 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8X9S_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (G), FASTA

>8X9S_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (R), FASTA

>8X9S_3 Adhesion G-protein coupled receptor D1 (chains R)
HPIITNLTEERKTFQSPGVILSYLQNVSLSLPSKSLSEQTALNLTKTFLKAVGEILLLPG
WIALSEDSAVVLSLIDTIDTVMGHVSSNLHGSTPQVTVEGSSAMAEFSVAKILPKTVNSS
HYRFPAHGQSFIQIPHEAFHRHAWSTVVGLLYHSMHYYLNNIWPAHTKIAEAMHHQDCLL
FATSHLISLEVSPPPTLSQNLSGSPLITVHLKHRLTRKQHSEATNSSNRVFVYCAFLDFS
SGEGVWSNHGCALTRGNLTYSVCRCTHLTNFAILMQVVPLELARGHQVALSSISYVGCSL
SVLCLVATLVTFAVLSSVSTIRNQRYHIHANLSFAVLVAQVLLLISFRLEPGTTPCQVMA
VLLHYFFLSAFAWMLVEGLHLYSMVIKVFGSEDSKHRYYYGMGWGFPLLICIISLSFAMD
SYGTSNNCWLSLASGAIWAFVAPALFVIVVNIGILIAVTRVISQISADNYKIHGDPSAFK
LTAKAVAVLLPILGTSWVFGVLAVNGCAVVFQYMFATLNSLQGLFIFLFHCLLNSEVRAA
FKHKTKVWSLTSSSARTSNAKPFHSDLMNGTRPGMASTKLSPWDKSSHSAHRVDLSAV

Sequence of entity 4 (A), FASTA

>8X9S_4 Gs protein alpha subunit (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L

Ligands and cofactors

ID	Name	Formula	Copies
DHT	5-alpha-dihydrotestosterone	C19 H30 O2	1

Primary citation

Identification, structure, and agonist design of an androgen membrane receptor. Yang, Z., Ping, Y.Q., Wang, M.W. et al. Cell (2025) 188:1589. DOI 10.1016/j.cell.2025.01.006 · PubMed

Other PDB entries of the same protein (UniProt P54311 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
9EJZ 2.06 Å, Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine…
9IJE 2.34 Å, Epinephrine-activated human beta3 adrenergic receptor
8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
7MBY 2.44 Å, Human Cholecystokinin 1 receptor (CCK1R) Gq chimera (mGsqi) complex
9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
8JIS 2.46 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist peptide15-bound human GLP-1R-Gs complex
9M0R 2.47 Å, Structure of neuropeptide FF receptor 1 complex with NPVF
8YKV 2.48 Å, Cryo-EM structure of succinate receptor SUCR1 bound to compound 31
9M1O 2.49 Å, Cryo-EM structures of NPFFR2 complex with neuropeptide FF

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