9EAH: Nanobody AT209

Structure of nanobody AT209 in complex with the olmesartan-bound angiotensin II type I receptor (AT1R). Determined by electron microscopy at 3.1 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Camelidae, Homo sapiens, Escherichia coli
Chains: 4
Atoms: 5,606
Mol. weight: 179.28 kDa
Ligands: CLR, OLM
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9EAH contains 25 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: 19 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	30-52	23
α-helix	53-57	5
α-helix	62-89	28
α-helix	97-131	35
α-helix	142-159	18
α-helix	161-165	5
β-strand	168-171	4	1
β-strand	178-181	4	1
β-strand	182-183	2	2
α-helix	191-199	9
α-helix	200-205	6
α-helix	206-244	39
α-helix	248-267	20
α-helix	283-304	22
α-helix	309-316	8
α-helix	319-322	4
α-helix	323-327	5
α-helix	328-339	12
α-helix	1237-1268	32
α-helix	1274-1291	18
α-helix	1294-1304	11
α-helix	1310-1314	5

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	8
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	68-71	4	8
β-strand	77-81	5	8
α-helix	87-89	3
β-strand	92-99	8	2
β-strand	105-107	3	2
β-strand	112-113	2	2

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	3
β-strand	14	1	4
β-strand	21-28	8	3
α-helix	32-34	3
β-strand	35-42	8	5
β-strand	48-55	8	5
β-strand	62-63	2	5
β-strand	72-76	5	3
β-strand	81-86	6	3
β-strand	96-103	8	5
α-helix	108-111	4
β-strand	118	1	3
β-strand	121-122	2	5
β-strand	124	1	4

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-6	2	6
β-strand	11-13	3	7
β-strand	20-26	7	6
β-strand	34-39	6	7
β-strand	46-50	5	7
β-strand	54-55	2	7
β-strand	63-68	6	6
β-strand	71-76	6	6
α-helix	81-83	3
β-strand	86-92	7	7
β-strand	98-100	3	7
β-strand	104-107	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody AT209,Type-1 angiotensin II receptor,Soluble cytochrome b562	A, B	protein	580	Camelidae, 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, B), FASTA

>9EAH_1 Nanobody AT209,Type-1 angiotensin II receptor,Soluble cytochrome b562 (chains A, B)
QVQLQESGGGLVQAGGSLRLSCAASGYIFYRYSMGWYRQAPGKEREFVAGISYGATTNYA
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAWGGRTLYFVYWGQGTQVTVSSGG
SGEDQVDPRLIDGKILNSSTEDGIKRIQDDCPKAGRHNYIFVMIPTLYSIIFVVGIFGNS
LVVIVIYFYMKLKTVASVFLLNLALADLCFLLTLPLWAVYTAMEYRWPFGNYLCKIASAS
VSFNLYASVFLLTCLSIDRYLAIVHPMKSRLRRTMLVAKVTCIIIWLLAGLASLPAIIHR
NVFFIENTNITVCAFHYESQNSTLPIGLGLTKNILGFLFPFLIILTSYTLIWKALKKAYD
LEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFR
HGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLDKLNDDIFK
IIMAIVLFFFFSWIPHQIFTFLDVLIQLGIIRDCRIADIVDTAMPITICIAYFNNCLNPL
FYGFLGKKFKRYFLQLLKYGGSSLEVLFQGPTETSQVAPA

Sequence of entity 2 (C), FASTA

>9EAH_2 BAG2 Anti-BRIL Fab Heavy Chain (chains C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (D), FASTA

>9EAH_3 BAG2 Anti-BRIL Fab Light Chain (chains D)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
OLM	Olmesartan	C24 H26 N6 O3	1

Primary citation

Epitope-directed selection of GPCR nanobody ligands with evolvable function. Skiba, M.A., Canavan, C., Nemeth, G.R. et al. Proc Natl Acad Sci U S A (2025) 122:e2423931122-e2423931122. DOI 10.1073/pnas.2423931122 · 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…
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)
9ZXD 3.2 Å, Structure of AT118-R nanobody in complex with the angiotensin II type I receptor bound…
8TH4 3.3 Å, Structure of AT118-L Nanobody Antagonist in Complex with the Angiotensin II Type I…

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