6VI4 | pdb_00006vi4

Nanobody-Enabled Monitoring of Kappa Opioid Receptor States

• PDB DOI: https://doi.org/10.2210/pdb6VI4/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2020-01-11 Released: 2020-03-18 
• Deposition Author(s): Che, T., Roth, B.L.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.271 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Nanobody-enabled monitoring of kappa opioid receptor states.

Che, T., English, J., Krumm, B.E., Kim, K., Pardon, E., Olsen, R.H.J., Wang, S., Zhang, S., Diberto, J.F., Sciaky, N., Carroll, F.I., Steyaert, J., Wacker, D., Roth, B.L.

(2020) Nat Commun 11: 1145-1145

• PubMed: 32123179 
• DOI: https://doi.org/10.1038/s41467-020-14889-7
• Primary Citation Related Structures: 
  6VI4


• PubMed Abstract: 
  

  Recent studies show that GPCRs rapidly interconvert between multiple states although our ability to interrogate, monitor and visualize them is limited by a relative lack of suitable tools. We previously reported two nanobodies (Nb39 and Nb6) that stabilize distinct ligand- and efficacy-delimited conformations of the kappa opioid receptor. Here, we demonstrate via X-ray crystallography a nanobody-targeted allosteric binding site by which Nb6 stabilizes a ligand-dependent inactive state. As Nb39 stabilizes an active-like state, we show how these two state-dependent nanobodies can provide real-time reporting of ligand stabilized states in cells in situ. Significantly, we demonstrate that chimeric GPCRs can be created with engineered nanobody binding sites to report ligand-stabilized states. Our results provide both insights regarding potential mechanisms for allosterically modulating KOR with nanobodies and a tool for reporting the real-time, in situ dynamic range of GPCR activity.

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Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA. [e-mail].
Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium.
VIB-VUB Center for Structural Biology, VIB, Brussels, 1050, Belgium.
State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
Research Triangle Institute, Research Triangle Park, Durham, NC, USA.
Department of Pharmacological Sciences and Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA. [e-mail].
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [e-mail].
National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 100.41 kDa 
• Atom Count: 6,047 
• Modeled Residue Count: 794 
• Deposited Residue Count: 880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa opioid receptor	A, B	307	Homo sapiens	Mutation(s): 1  Gene Names: OPRK1, OPRK Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens) Explore P41145  Go to UniProtKB:  P41145
PHAROS:  P41145 GTEx:  ENSG00000082556

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 6	C, D	133	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JDC (Subject of Investigation/LOI)	E [auth A], F [auth B]	(3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide C28 H39 N3 O3 ZLVXBBHTMQJRSX-VMGNSXQWSA-N
CLR	G [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JDC	BindingDB:  6VI4	Ki: min: 1.00e-2, max: 0.32 (nM) from 7 assay(s)
		EC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.271 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.394	α = 90
b = 108.191	β = 90
c = 155.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Che, T., Roth, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)		--

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary