8UEK | pdb_00008uek

Solution structure of ACKR3-targeting nanobody VUN701

• PDB DOI: https://doi.org/10.2210/pdb8UEK/pdb
• BMRB: 31108

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-01 Released: 2024-06-12 
• Deposition Author(s): Schlimgen, R.R., Peterson, F.C., Volkman, B.F.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Structural basis for selectivity and antagonism in extracellular GPCR-nanobodies.

Schlimgen, R.R., Peterson, F.C., Heukers, R., Smit, M.J., McCorvy, J.D., Volkman, B.F.

(2024) Nat Commun 15: 4611-4611

• PubMed: 38816420 
• DOI: https://doi.org/10.1038/s41467-024-49000-x
• Primary Citation Related Structures: 
  8UEK


• PubMed Abstract: 
  

  G protein-coupled receptors (GPCRs) are pivotal therapeutic targets, but their complex structure poses challenges for effective drug design. Nanobodies, or single-domain antibodies, have emerged as a promising therapeutic strategy to target GPCRs, offering advantages over traditional small molecules and antibodies. However, an incomplete understanding of the structural features enabling GPCR-nanobody interactions has limited their development. In this study, we investigate VUN701, a nanobody antagonist targeting the atypical chemokine receptor 3 (ACKR3). We determine that an extended CDR3 loop is required for ACKR3 binding. Uncommon in most nanobodies, an extended CDR3 is prevalent in GPCR-targeting nanobodies. Combining experimental and computational approaches, we map an inhibitory ACKR3-VUN701 interface and define a distinct conformational mechanism for GPCR inactivation. Our results provide insights into class A GPCR-nanobody selectivity and suggest a strategy for the development of these new therapeutic tools.

---

Organizational Affiliation: 
• Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
Amsterdam Institute of Molecular and Life Sciences, Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit, 1081 HZ, Amsterdam, The Netherlands.
Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 13.32 kDa 
• Atom Count: 934 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACKR3-targeting nanobody VUN701	A	124	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Schlimgen, R.R., Peterson, F.C., Volkman, B.F.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI058072

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary