8TH3: AT118-H Nanobody Antagonist

Structure of AT118-H Nanobody Antagonist in Complex with the Angiotensin II Type I Receptor. Determined by electron microscopy at 3.0 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Camelidae, Homo sapiens, Escherichia coli
Chains: 4
Atoms: 5,770
Mol. weight: 179.78 kDa
Ligands: Y01
Released: 22 May 2024

Explore 8TH3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TH3 contains 29 α-helices and 33 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: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-51	28
α-helix	52-56	5
α-helix	62-80	19
α-helix	83-89	7
α-helix	98-131	34
α-helix	139-158	20
α-helix	162-165	4
β-strand	167-171	5	1
β-strand	178-184	7	1
α-helix	191-200	10
α-helix	201-205	5
α-helix	206-243	38
α-helix	250-266	17
α-helix	284-305	22
α-helix	310-315	6
α-helix	318-322	5
α-helix	323-327	5
α-helix	328-341	14
α-helix	1237-1252	16
α-helix	1254-1268	15
α-helix	1274-1301	28
α-helix	1307-1309	3
α-helix	1310-1315	6

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	2
α-helix	26-31	6
β-strand	33-39	7	1
β-strand	46-51	6	1
β-strand	58-59	2	1
β-strand	68-69	2	2
β-strand	77-82	6	2
β-strand	92-99	8	1
β-strand	105-107	3	1
β-strand	112-113	2	1

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	3
β-strand	13-14	2	4
β-strand	21-28	8	3
β-strand	35-42	8	4
β-strand	48-54	7	4
β-strand	62-63	2	4
β-strand	71-76	6	3
β-strand	81-86	6	3
α-helix	91-93	3
β-strand	95-103	9	4
α-helix	108-111	4
β-strand	118	1	3
β-strand	121-124	4	4

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-7	3	5
β-strand	11-12	2	6
β-strand	20-26	7	5
β-strand	34-39	6	7
α-helix	40	1
β-strand	46-50	5	7
β-strand	54-55	2	7
α-helix	56	1
β-strand	63-68	6	5
β-strand	71-76	6	5
α-helix	81-83	3
β-strand	86-91	6	7
α-helix	95-97	3
β-strand	99-100	2	7
β-strand	105-106	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AT118-H nanobody, Type-1 angiotensin II receptor, Soluble cytochrome b562 complex	A, B	protein	582	Camelidae, 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

Sequence of entity 1 (A, B), FASTA

>8TH3_1 AT118-H nanobody, Type-1 angiotensin II receptor, Soluble cytochrome b562 complex (chains A, B)
EVQLVESGGGLVQPGGSLRLSCAASGYIYRRYRMGWYRQAPGKGREFVAAISGGSSTNYA
DSVKGRFTISRDNSKNTVYLQMNSLRAEDTAVYYCAAYRIVSDPRVYWGQGTQVTVSSLE
GGSGEDQVDPRLIDGKILNSSTEDGIKRIQDDCPKAGRHNYIFVMIPTLYSIIFVVGIFG
NSLVVIVIYFYMKLKTVASVFLLNLALADLCFLLTLPLWAVYTAMEYRWPFGNYLCKIAS
ASVSFNLYASVFLLTCLSIDRYLAIVHPMKSRLRRTMLVAKVTCIIIWLLAGLASLPAII
HRNVFFIENTNITVCAFHYESQNSTLPIGLGLTKNILGFLFPFLIILTSYTLIWKALKKA
YDLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKD
FRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLDKLNDDI
FKIIMAIVLFFFFSWIPHQIFTFLDVLIQLGIIRDCRIADIVDTAMPITICIAYFNNCLN
PLFYGFLGKKFKRYFLQLLKYGGSSLEVLFQGPTETSQVAPA

Sequence of entity 2 (C), FASTA

>8TH3_2 BAG2 Anti-BRIL Fab Heavy Chain (chains C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (D), FASTA

>8TH3_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	2

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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