8X9U: PDB entry 8X9U

Identification, structure and agonist design of an androgen membrane receptor. Determined by electron microscopy at 2.88 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Rattus norvegicus, Bos taurus, synthetic construct
Chains: 5
Atoms: 8,243
Mol. weight: 182.3 kDa
Ligands: A1LU1
Released: 12 Feb 2025

Explore 8X9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X9U contains 37 α-helices and 61 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	40-45	6	15
α-helix	53-59	7
β-strand	207-213	7	15
β-strand	218-224	7	15
α-helix	234-238	5
β-strand	243-248	6	15
α-helix	254-266	3
α-helix	267-277	11
β-strand	286-291	6	15
α-helix	294-302	9
α-helix	308-311	4
α-helix	335-348	14
β-strand	359-363	5	15
α-helix	371-390	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	38-39	2
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	88-94	7	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	165-170	6	4
β-strand	175-180	6	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-223	6	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	249-254	6	6
β-strand	259-264	6	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	303-308	6	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	335-339	5	1

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	27-29	3
α-helix	35-42	8
α-helix	56-58	3

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	565-590	26
α-helix	595-597	3
α-helix	600-622	23
α-helix	626-627	2
α-helix	630-637	8
α-helix	644-661	18
α-helix	675-678	4
α-helix	682-693	12
α-helix	696-698	3
α-helix	711-713	3
α-helix	714-742	29
α-helix	754-769	16
α-helix	771-773	3
α-helix	774-778	5
α-helix	787-795	9
α-helix	798-803	6
α-helix	804-808	5
α-helix	811-826	16

Chain S: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	8
β-strand	6-7	2	9
β-strand	11-12	2	10
β-strand	18-23	6	9
β-strand	25	1	8
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	69-73	5	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	93-99	7	11
β-strand	111	1	11
β-strand	115	1	11
β-strand	118-119	2	10
α-helix	126-127	2
β-strand	128-129	2	12
β-strand	134-135	2	13
β-strand	142-149	8	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
α-helix	184	1
β-strand	191-195	5	12
β-strand	199-205	7	12
β-strand	214-219	6	13
β-strand	227	1	13
β-strand	231-233	3	13

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)
scFv16	S	protein	267	synthetic construct
Gs protein alpha subunit	A	protein	361	Bos taurus
Adhesion G-protein coupled receptor D1	R	protein	598	Homo sapiens	Q6QNK2 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8X9U_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

>8X9U_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (S), FASTA

>8X9U_3 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELLEENLYFQGASHHHHHHHH

Sequence of entity 4 (A), FASTA

>8X9U_4 Gs protein alpha subunit (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L

Sequence of entity 5 (R), FASTA

>8X9U_5 Adhesion G-protein coupled receptor D1 (chains R)
HPIITNLTEERKTFQSPGVILSYLQNVSLSLPSKSLSEQTALNLTKTFLKAVGEILLLPG
WIALSEDSAVVLSLIDTIDTVMGHVSSNLHGSTPQVTVEGSSAMAEFSVAKILPKTVNSS
HYRFPAHGQSFIQIPHEAFHRHAWSTVVGLLYHSMHYYLNNIWPAHTKIAEAMHHQDCLL
FATSHLISLEVSPPPTLSQNLSGSPLITVHLKHRLTRKQHSEATNSSNRVFVYCAFLDFS
SGEGVWSNHGCALTRGNLTYSVCRCTHLTNFAILMQVVPLELARGHQVALSSISYVGCSL
SVLCLVATLVTFAVLSSVSTIRNQRYHIHANLSFAVLVAQVLLLISFRLEPGTTPCQVMA
VLLHYFFLSAFAWMLVEGLHLYSMVIKVFGSEDSKHRYYYGMGWGFPLLICIISLSFAMD
SYGTSNNCWLSLASGAIWAFVAPALFVIVVNIGILIAVTRVISQISADNYKIHGDPSAFK
LTAKAVAVLLPILGTSWVFGVLAVNGCAVVFQYMFATLNSLQGLFIFLFHCLLNSEVRAA
FKHKTKVWSLTSSSARTSNAKPFHSDLMNGTRPGMASTKLSPWDKSSHSAHRVDLSAV

Ligands and cofactors

ID	Name	Formula	Copies
A1LU1	Metenolone	C20 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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