6Z66 | pdb_00006z66

Crystal structure of apo-state neurotensin receptor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.294 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.286 (Depositor), 0.286 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 53.09 kDa 
  • Atom Count: 3,241 
  • Modeled Residue Count: 459 
  • Deposited Residue Count: 482 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.294 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.286 (Depositor), 0.286 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.186α = 90
b = 212.992β = 90
c = 94.639γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary