RCSB PDB - 6Z4Q: Crystal structure of the neurotensin receptor 1 in complex with the small-molecule inverse agonist SR142948A

 6Z4Q

Crystal structure of the neurotensin receptor 1 in complex with the small-molecule inverse agonist SR142948A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.281 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism.

Deluigi, M.Klipp, A.Klenk, C.Merklinger, L.Eberle, S.A.Morstein, L.Heine, P.Mittl, P.R.E.Ernst, P.Kamenecka, T.M.He, Y.Vacca, S.Egloff, P.Honegger, A.Pluckthun, A.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abe5504
  • Primary Citation of Related Structures:  
    6YVR, 6Z4Q, 6Z4S, 6Z4V, 6Z66, 6Z8N, 6ZA8, 6ZIN

  • PubMed Abstract: 

    Neurotensin receptor 1 (NTSR1) and related G protein-coupled receptors of the ghrelin family are clinically unexploited, and several mechanistic aspects of their activation and inactivation have remained unclear. Enabled by a new crystallization design, we present five new structures: apo-state NTSR1 as well as complexes with nonpeptide inverse agonists SR48692 and SR142948A, partial agonist RTI-3a, and the novel full agonist SRI-9829, providing structural rationales on how ligands modulate NTSR1. The inverse agonists favor a large extracellular opening of helices VI and VII, undescribed so far for NTSR1, causing a constriction of the intracellular portion. In contrast, the full and partial agonists induce a binding site contraction, and their efficacy correlates with the ability to mimic the binding mode of the endogenous agonist neurotensin. Providing evidence of helical and side-chain rearrangements modulating receptor activation, our structural and functional data expand the mechanistic understanding of NTSR1 and potentially other peptidergic receptors.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurotensin receptor type 1,Neurotensin receptor type 1,DARPinA [auth AAA]482Rattus norvegicussynthetic construct
This entity is chimeric
Mutation(s): 26 
Gene Names: Ntsr1Ntsr
Membrane Entity: Yes 
UniProt
Find proteins for P20789 (Rattus norvegicus)
Explore P20789 
Go to UniProtKB:  P20789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20789
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q6N (Subject of Investigation/LOI)
Query on Q6N

Download Ideal Coordinates CCD File 
B [auth AAA]2-[[5-(2,6-dimethoxyphenyl)-1-[4-[3-(dimethylamino)propyl-methyl-carbamoyl]-2-propan-2-yl-phenyl]pyrazol-3-yl]carbonylamino]adamantane-2-carboxylic acid
C39 H51 N5 O6
LWULHXVBLMWCHO-MWKTWYAFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Q6N BindingDB:  6Z4Q Kd: 0.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.281 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.924α = 90
b = 36.845β = 113.65
c = 90.288γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q6NClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_182334

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-03-17
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary