5DHG | pdb_00005dhg

The crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with C-35 (PSI Community Target)

• PDB DOI: https://doi.org/10.2210/pdb5DHG/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2015-08-30 Released: 2015-10-21 
• Deposition Author(s): Miller, R.L., Thompson, A.A., Trapella, C., Guerrini, R., Malfacini, D., Patel, N., Han, G.W., Cherezov, V., Calo, G., Katritch, V., Stevens, R.C., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.275 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor.

Miller, R.L., Thompson, A.A., Trapella, C., Guerrini, R., Malfacini, D., Patel, N., Han, G.W., Cherezov, V., Calo, G., Katritch, V., Stevens, R.C.

(2015) Structure 23: 2291-2299

• PubMed: 26526853 
• DOI: https://doi.org/10.1016/j.str.2015.07.024
• Primary Citation Related Structures: 
  5DHG, 5DHH


• PubMed Abstract: 
  

  Understanding the mechanism by which ligands affect receptor conformational equilibria is key in accelerating membrane protein structural biology. In the case of G protein-coupled receptors (GPCRs), we currently pursue a brute-force approach for identifying ligands that stabilize receptors and facilitate crystallogenesis. The nociceptin/orphanin FQ peptide receptor (NOP) is a member of the opioid receptor subfamily of GPCRs for which many structurally diverse ligands are available for screening. We observed that antagonist potency is correlated with a ligand's ability to induce receptor stability (Tm) and crystallogenesis. Using this screening strategy, we solved two structures of NOP in complex with top candidate ligands SB-612111 and C-35. Docking studies indicate that while potent, stabilizing antagonists strongly favor a single binding orientation, less potent ligands can adopt multiple binding modes, contributing to their low Tm values. These results suggest a mechanism for ligand-aided crystallogenesis whereby potent antagonists stabilize a single ligand-receptor conformational pair.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Chemical and Pharmaceutical Sciences and LTTA (Laboratorio per le Tecnologie delle Terapie Avanzate), University of Ferrara, 44121 Ferrara, Italy.
Department of Medical Sciences, Section of Pharmacology and National Institute of Neuroscience, University of Ferrara, 44121 Ferrara, Italy.
Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.11 kDa 
• Atom Count: 5,071 
• Modeled Residue Count: 660 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Nociceptin receptor	A, B	424	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: cybC, OPRL1, OOR, ORL1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P41146 (Homo sapiens) Explore P41146  Go to UniProtKB:  P41146
PHAROS:  P41146 GTEx:  ENSG00000125510
UniProt Groups	P41146P0ABE7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGV	C [auth A], G [auth B]	1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide C26 H33 Cl2 N3 O UWHDLFOAIARROU-XMMPIXPASA-N
OLC	H [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DGV	BindingDB:  5DHG	Ki: 0.72 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.275 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.079	α = 90
b = 171.696	β = 103.25
c = 66.491	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Miller, R.L., Thompson, A.A., Trapella, C., Guerrini, R., Malfacini, D., Patel, N., Han, G.W., Cherezov, V., Calo, G., Katritch, V., Stevens, R.C., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references
• Version 1.2: 2015-12-16
  Changes: Database references
• Version 1.3: 2016-03-02
  Changes: Database references
• Version 1.4: 2017-05-31
  Changes: Source and taxonomy
• Version 1.5: 2017-07-05
  Changes: Database references
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-10-16
  Changes: Structure summary