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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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
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

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Ligand Structure Quality Assessment 


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