8TH4

Structure of AT118-L Nanobody Antagonist in Complex with the Angiotensin II Type I Receptor and Losartan

  • Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
  • Organism(s): Homo sapiens, Escherichia coli, synthetic construct
  • Expression System: Homo sapiens, Escherichia coli BL21(DE3)
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2023-07-13 Released: 2024-05-22 
  • Deposition Author(s): Skiba, M.A., Kruse, A.C.
  • Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD), National Institutes of Health/National Cancer Institute (NIH/NCI), The Vallee Foundation Inc., Richard and Susan Smith Family Foundation, National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), The Pew Charitable Trusts

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Antibodies expand the scope of angiotensin receptor pharmacology.

Skiba, M.A.Sterling, S.M.Rawson, S.Zhang, S.Xu, H.Jiang, H.Nemeth, G.R.Gilman, M.S.A.Hurley, J.D.Shen, P.Staus, D.P.Kim, J.McMahon, C.Lehtinen, M.K.Rockman, H.A.Barth, P.Wingler, L.M.Kruse, A.C.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01620-6
  • Primary Citation of Related Structures:  
    8TH3, 8TH4

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often limited at the receptor, tissue and cellular levels. Antibodies have the potential to address these limitations but their properties as GPCR ligands remain poorly characterized. Here, using protein engineering, pharmacological assays and structural studies, we develop maternally selective heavy-chain-only antibody ('nanobody') antagonists against the angiotensin II type I receptor and uncover the unusual molecular basis of their receptor antagonism. We further show that our nanobodies can simultaneously bind to angiotensin II type I receptor with specific small-molecule antagonists and demonstrate that ligand selectivity can be readily tuned. Our work illustrates that antibody fragments can exhibit rich and evolvable pharmacology, attesting to their potential as next-generation GPCR modulators.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type-1 angiotensin II receptor Soluble cytochrome b562 complex433Homo sapiensEscherichia coliMutation(s): 2 
Gene Names: AGTR1AGTR1AAGTR1BAT2R1AT2R1BcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30556 (Homo sapiens)
Explore P30556 
Go to UniProtKB:  P30556
PHAROS:  P30556
GTEx:  ENSG00000144891 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P30556
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BAG2 Anti-BRIL Fab Heavy ChainB [auth C]231synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BAG2 Anti-BRIL Fab Light ChainC [auth D]215synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AT118-L NanobodyD [auth B]140synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LSN
Query on LSN

Download Ideal Coordinates CCD File 
E [auth A][2-butyl-5-chloranyl-3-[[4-[2-(2H-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]imidazol-4-yl]methanol
C22 H23 Cl N6 O
PSIFNNKUMBGKDQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesOD021345
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesHD101596
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA260415
The Vallee Foundation Inc.United States--
Richard and Susan Smith Family FoundationUnited States--
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS088566
The Pew Charitable TrustsUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references