9ZXD: AT118-R nanobody

Structure of AT118-R nanobody in complex with the angiotensin II type I receptor bound to L-162,313. Determined by electron microscopy at 3.2 Å resolution. Released 29 Jul 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: synthetic construct, Homo sapiens, Escherichia coli
Chains: 3
Atoms: 5,738
Mol. weight: 114.54 kDa
Ligands: Y01, A1C42
Released: 29 Jul 2026

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

Secondary structure: helices and β-sheets

9ZXD contains 26 α-helices and 34 β-strands across 3 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: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	-116--112	5	1
α-helix	-109--104	6
β-strand	-102--96	7	2
β-strand	-90--84	7	2
β-strand	-77--76	2	2
β-strand	-68--63	6	1
β-strand	-58--53	6	1
β-strand	-43--37	7	2
β-strand	-30--28	3	2
β-strand	-23	1	2
α-helix	26-29	4
α-helix	31-51	21
α-helix	52-56	5
α-helix	63-79	17
α-helix	81-89	9
α-helix	98-131	34
α-helix	142-159	18
α-helix	161-166	6
β-strand	167-171	5	2
β-strand	178-184	7	2
α-helix	191-200	10
α-helix	201-205	5
α-helix	206-243	38
α-helix	248-267	20
α-helix	271-274	4
α-helix	281-305	25
α-helix	309-316	8
α-helix	319-322	4
α-helix	323-327	5
α-helix	328-339	12
α-helix	1237-1267	31
α-helix	1277-1291	15
α-helix	1294-1305	12
α-helix	1307-1310	4

Chain C: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	3
β-strand	20-28	9	3
β-strand	35-42	8	4
β-strand	49-55	7	4
β-strand	60-63	4	4
β-strand	71-76	6	3
β-strand	81-87	7	3
α-helix	91-93	3
β-strand	95-103	9	4
α-helix	108-111	4
β-strand	117	1	4
β-strand	121-123	3	4

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-7	3	5
β-strand	20-26	7	5
β-strand	30	1	6
β-strand	32	1	6
β-strand	34	1	7
β-strand	36-39	4	8
β-strand	47-50	4	8
β-strand	54-55	2	8
β-strand	63-68	6	5
β-strand	71-76	6	5
β-strand	86-88	3	8
β-strand	90-92	3	7
β-strand	98-100	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion	A	protein	582	synthetic construct, Homo sapiens, Escherichia coli	P30556 (AlphaFold model)
BAG2 Anti-BRIL Fab Heavy Chain	C	protein	231	synthetic construct
BAG2 Anti-BRIL Fab Light Chain	D	protein	215	synthetic construct

Sequence of entity 1 (A), FASTA

>9ZXD_1 AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion (chains A)
QVQLQESGGGLVQAGGSLRLSCAASGYIYRKYRMGWYRQAPGKEREFVAGINGGSSTNYA
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAYRIVRGLLVYWGQGTQVTVSSLE
GGSGEDQVDPRLIDGKILNSSTEDGIKRIQDDCPKAGRHNYIFVMIPTLYSIIFVVGIFG
NSLVVIVIYFYMKLKTVASVFLLNLALADLCFLLTLPLWAVYTAMEYRWPFGNYLCKIAS
ASVSFNLYASVFLLTCLSIDRYLAIVHPMKSRLRRTMLVAKVTCIIIWLLAGLASLPAII
HRNVFFIENTNITVCAFHYESQNSTLPIGLGLTKNILGFLFPFLIILTSYTLIWKALKKA
YDLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKD
FRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLDKLNDDI
FKIIMAIVLFFFFSWIPHQIFTFLDVLIQLGIIRDCRIADIVDTAMPITICIAYFNNCLN
PLFYGFLGKKFKRYFLQLLKYGGSSLEVLFQGPTETSQVAPA

Sequence of entity 2 (C), FASTA

>9ZXD_2 BAG2 Anti-BRIL Fab Heavy Chain (chains C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (D), FASTA

>9ZXD_3 BAG2 Anti-BRIL Fab Light Chain (chains D)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	1
A1C42	butyl [3-{4-[(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)methyl]phenyl}…	C30 H38 N4 O4 S2	1

Primary citation

Activation of the angiotensin II type I receptor by a nonpeptide agonist. Skiba, M.A., Liu, J., Shen, P. et al. Proc Natl Acad Sci U S A (2026) 123:e2602538123-e2602538123. DOI 10.1073/pnas.2602538123 · PubMed

Other PDB entries of the same protein (UniProt P30556 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6OS2 2.7 Å, Structure of synthetic nanobody-stabilized angiotensin II type 1 receptor bound to TRV026
6OS1 2.79 Å, Structure of synthetic nanobody-stabilized angiotensin II type 1 receptor bound to TRV023
4ZUD 2.8 Å, Crystal Structure of Human Angiotensin Receptor in Complex with Inverse Agonist…
4YAY 2.9 Å, XFEL structure of human Angiotensin Receptor
6OS0 2.9 Å, Structure of synthetic nanobody-stabilized angiotensin II type 1 receptor bound to…
6DO1 2.9 Å, Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8
8TH3 3.0 Å, Structure of AT118-H Nanobody Antagonist in Complex with the Angiotensin II Type I…
9Q0F 3.02 Å, Structure of angiotensin II type 1 receptor bound to a b-arrestin biased allosteric…
9EAH 3.1 Å, Structure of nanobody AT209 in complex with the olmesartan-bound angiotensin II type I…
9EAI 3.1 Å, Structure of nanobody AT206 in complex with the losartan-bound angiotensin II type I…
9EAJ 3.2 Å, Structure of nanobody AT206 in complex with the angiotensin II type I receptor (AT1R)
8TH4 3.3 Å, Structure of AT118-L Nanobody Antagonist in Complex with the Angiotensin II Type I…

Browse structure collections

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