6VI4

Nanobody-Enabled Monitoring of Kappa Opioid Receptor States


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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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

  • DOI: 10.1038/s41467-020-14889-7
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    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. bryan_roth@med.unc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kappa opioid receptorA, B307Homo sapiensMutation(s): 1 
Gene Names: OPRK1OPRK
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens)
Explore P41145 
Go to UniProtKB:  P41145
PHAROS:  P41145
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41145
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 6C, D133Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JDC (Subject of Investigation/LOI)
Query on JDC

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth B]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JDC BindingDB:  6VI4 Ki: min: 1.00e-2, max: 0.41 (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 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.394α = 90
b = 108.191β = 90
c = 155.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release