8TH4: AT118-L Nanobody Antagonist

Structure of AT118-L Nanobody Antagonist in Complex with the Angiotensin II Type I Receptor and Losartan. Determined by electron microscopy at 3.3 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli, synthetic construct
Chains: 4
Atoms: 5,702
Mol. weight: 113.35 kDa
Ligands: LSN
Released: 22 May 2024

Explore 8TH4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TH4 contains 23 α-helices and 34 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: 20 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-28	5
α-helix	31-55	25
α-helix	62-89	28
α-helix	98-131	34
α-helix	141-159	19
α-helix	161-165	5
β-strand	167-171	5	1
β-strand	178-184	7	1
α-helix	191-198	8
α-helix	199-203	5
α-helix	205-244	40
α-helix	250-266	17
α-helix	284-306	23
α-helix	309-322	14
α-helix	323-327	5
α-helix	328-339	12
α-helix	1237-1252	16
α-helix	1254-1267	14
α-helix	1274-1291	18
α-helix	1293-1296	4
α-helix	1300-1305	6
α-helix	1307-1311	5

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	6
β-strand	19-23	5	7
β-strand	24	1	6
α-helix	26-30	5
β-strand	33-39	7	1
β-strand	45-50	6	1
β-strand	58-59	2	1
β-strand	67-72	6	7
β-strand	77-82	6	7
β-strand	91-99	9	1
β-strand	105-107	3	1
β-strand	112-114	3	1

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	2
β-strand	13-14	2	3
β-strand	24-28	5	2
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-55	8	3
β-strand	60-63	4	3
β-strand	72-76	5	2
β-strand	81-85	5	2
β-strand	95-102	8	3
β-strand	117	1	3
β-strand	121-124	4	3

Chain D: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	20-26	7	4
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
α-helix	56	1
β-strand	63-68	6	4
β-strand	71-76	6	4
β-strand	86-91	6	5
β-strand	99-100	2	5
β-strand	104-105	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Type-1 angiotensin II receptor Soluble cytochrome b562 complex	A	protein	433	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), 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
AT118-L Nanobody	B	protein	140	synthetic construct

Sequence of entity 1 (A), FASTA

>8TH4_1 Type-1 angiotensin II receptor Soluble cytochrome b562 complex (chains A)
DYKDDDDKILNSSTEDGIKRIQDDCPKAGRHNYIFVMIPTLYSIIFVVGIFGNSLVVIVI
YFYMKLKTVASVFLLNLALADLCFLLTLPLWAVYTAMEYRWPFGNYLCKIASASVSFNLY
ASVFLLTCLSIDRYLAIVHPMKSRLRRTMLVAKVTCIIIWLLAGLASLPAIIHRNVFFIE
NTNITVCAFHYESQNSTLPIGLGLTKNILGFLFPFLIILTSYTLIWKALKKAYDLEDNWE
TLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDIL
VGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLDKLNDDIFKIIMAIV
LFFFFSWIPHQIFTFLDVLIQLGIIRDCRIADIVDTAMPITICIAYFNNCLNPLFYGFLG
KKFKRYFLQLLKY

Sequence of entity 2 (C), FASTA

>8TH4_2 BAG2 Anti-BRIL Fab Heavy Chain (chains C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (D), FASTA

>8TH4_3 BAG2 Anti-BRIL Fab Light Chain (chains D)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (B), FASTA

>8TH4_4 AT118-L Nanobody (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGYIYSRYRMGWYRQAPGKGREFVAAISGGSSTNYA
DSVKGRFTISRDNSKNTVYLQMNSLRAEDTAVYYCAAYKIDSNPRVYWGQGTQVTVSSGK
PIPNPLLGLDSTLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
LSN	[2-butyl-5-chloranyl-3-[[4-[2-(2H-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]im…	C22 H23 Cl N6 O	1

Primary citation

Antibodies expand the scope of angiotensin receptor pharmacology. Skiba, M.A., Sterling, S.M., Rawson, S. et al. Nat Chem Biol (2024) 20:1577-1585. DOI 10.1038/s41589-024-01620-6 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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