9IV1: ScFv16

Identification, structure and agonist design of an androgen membrane receptor. Determined by electron microscopy at 2.98 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.98 Å
Organisms: synthetic construct, Homo sapiens
Chains: 5
Atoms: 8,284
Mol. weight: 150.84 kDa
Ligands: DHT
Released: 12 Feb 2025

Explore 9IV1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IV1 contains 27 α-helices and 57 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	14-37	24
β-strand	40-46	7	14
α-helix	53-57	5
β-strand	207-214	8	14
β-strand	217-224	8	14
α-helix	235-237	3
β-strand	243-248	6	14
α-helix	267-277	11
β-strand	286-291	6	14
α-helix	296-302	7
α-helix	308-311	4
α-helix	334-349	16
β-strand	359-363	5	14
α-helix	369-371	3
α-helix	372-390	19

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-41	4
β-strand	47-51	5	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	78-83	6	7
β-strand	88-94	7	7
β-strand	100-105	6	8
β-strand	111-116	6	8
β-strand	123-125	3	8
β-strand	134-137	4	8
β-strand	146-151	6	9
β-strand	156-161	6	9
β-strand	165-170	6	9
β-strand	175-181	7	9
β-strand	189-192	4	10
β-strand	198-202	5	10
β-strand	207-212	6	10
β-strand	216-223	8	10
β-strand	232-234	3	11
β-strand	240-243	4	11
β-strand	250-254	5	11
β-strand	260-264	5	11
β-strand	276-278	3	12
β-strand	285-288	4	12
β-strand	293	1	13
β-strand	294-298	5	12
β-strand	303-306	4	12
β-strand	309	1	13
β-strand	315-320	6	6
β-strand	327-331	5	6
β-strand	336-339	4	6

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-23	18
α-helix	30-43	14

Chain R: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	568-590	23
α-helix	601-621	21
α-helix	630-657	28
α-helix	658-662	5
α-helix	672-679	8
α-helix	682-691	10
α-helix	721-740	20
α-helix	755-769	15
α-helix	773-776	4
α-helix	790-793	4
α-helix	798-806	9
α-helix	811-826	16

Chain S: 1 helix, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
β-strand	12	1	2
β-strand	18-21	4	1
β-strand	35-39	5	3
β-strand	45-51	7	3
β-strand	58-60	3	3
β-strand	68-73	6	1
β-strand	78-83	6	1
β-strand	95-98	4	3
β-strand	110-111	2	3
β-strand	119	1	2
β-strand	128-129	2	4
β-strand	134-136	3	5
β-strand	143-149	7	4
β-strand	162-167	6	5
β-strand	174-178	5	5
β-strand	182-183	2	5
α-helix	184	1
β-strand	191-195	5	4
β-strand	199-204	6	4
β-strand	213-219	7	5
β-strand	231-234	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
scFv16	S	protein	267	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	344	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Adhesion G-protein coupled receptor D1	R	protein	313	Homo sapiens	Q6QNK2 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	361	Homo sapiens	P63092 (AlphaFold model)

Sequence of entity 1 (S), FASTA

>9IV1_1 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELLEENLYFQGASHHHHHHHH

Sequence of entity 2 (B), FASTA

>9IV1_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 (G), FASTA

>9IV1_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>9IV1_4 Adhesion G-protein coupled receptor D1 (chains R)
HQVALSSISYVGCSLSVLCLVATLVTFAVLSSVSTIRNQRYHIHANLSFAVLVAQVLLLI
SFRLEPGTTPCQVMAVLLHYFFLSAFAWMLVEGLHLYSMVIKVFGSEDSKHRYYYGMGWG
FPLLICIISLSFAMDSYGTSNNCWLSLASGAIWAFVAPALFVIVVNIGILIAVTRVISQI
SADNYKIHGDPSAFKLTAKAVAVLLPILGTSWVFGVLAVNGCAVVFQYMFATLNSLQGLF
IFLFHCLLNSEVRAAFKHKTKVWSLTSSSARTSNAKPFHSDLMNGTRPGMASTKLSPWDK
SSHSAHRVDLSAV

Sequence of entity 5 (A), FASTA

>9IV1_5 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (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 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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