6B73

Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor.

Che, T.Majumdar, S.Zaidi, S.A.Ondachi, P.McCorvy, J.D.Wang, S.Mosier, P.D.Uprety, R.Vardy, E.Krumm, B.E.Han, G.W.Lee, M.Y.Pardon, E.Steyaert, J.Huang, X.P.Strachan, R.T.Tribo, A.R.Pasternak, G.W.Carroll, F.I.Stevens, R.C.Cherezov, V.Katritch, V.Wacker, D.Roth, B.L.

(2018) Cell 172: 55-67.e15

  • DOI: 10.1016/j.cell.2017.12.011

  • PubMed Abstract: 
  • The κ-opioid receptor (KOP) mediates the actions of opioids with hallucinogenic, dysphoric, and analgesic activities. The design of KOP analgesics devoid of hallucinatory and dysphoric effects has been hindered by an incomplete structural and mechani ...

    The κ-opioid receptor (KOP) mediates the actions of opioids with hallucinogenic, dysphoric, and analgesic activities. The design of KOP analgesics devoid of hallucinatory and dysphoric effects has been hindered by an incomplete structural and mechanistic understanding of KOP agonist actions. Here, we provide a crystal structure of human KOP in complex with the potent epoxymorphinan opioid agonist MP1104 and an active-state-stabilizing nanobody. Comparisons between inactive- and active-state opioid receptor structures reveal substantial conformational changes in the binding pocket and intracellular and extracellular regions. Extensive structural analysis and experimental validation illuminate key residues that propagate larger-scale structural rearrangements and transducer binding that, collectively, elucidate the structural determinants of KOP pharmacology, function, and biased signaling. These molecular insights promise to accelerate the structure-guided design of safer and more effective κ-opioid receptor therapeutics.


    Organizational Affiliation

    Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562, kappa-type opioid receptor
A, B
418Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 4 
Gene Names: OPRK1 (OPRK), cybC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
κ-opioid receptor in complex with JDTic
Find proteins for P41145 (Homo sapiens)
Go to Gene View: OPRK1
Go to UniProtKB:  P41145
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody
C, D
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CVV
Query on CVV

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Download CCD File 
A, B
N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide
C27 H27 I N2 O3
WTIFKSFIQUZRRN-JXGKSYOJSA-N
 Ligand Interaction
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A, B
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.310α = 90.00
b = 150.750β = 105.66
c = 100.280γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
BUSTERrefinement
PHASERphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental HealthUnited StatesRO1MH61887, U19MH82441

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references