7UL2

CryoEM Structure of Inactive NTSR1 Bound to SR48692 and Nb6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structure determination of inactive-state GPCRs with a universal nanobody.

Robertson, M.J.Papasergi-Scott, M.M.He, F.Seven, A.B.Meyerowitz, J.G.Panova, O.Peroto, M.C.Che, T.Skiniotis, G.

(2022) Nat Struct Mol Biol 29: 1188-1195

  • DOI: https://doi.org/10.1038/s41594-022-00859-8
  • Primary Citation of Related Structures:  
    7UL2, 7UL3, 7UL4, 7UL5

  • PubMed Abstract: 

    Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite representing one of the largest classes of therapeutic targets, most inactive-state G protein-coupled receptors (GPCRs) have remained inaccessible for cryo-EM because their small size and membrane-embedded nature impedes projection alignment for high-resolution map reconstructions. Here we demonstrate that the same single-chain camelid antibody (nanobody) recognizing a grafted intracellular loop can be used to obtain cryo-EM structures of inactive-state GPCRs at resolutions comparable or better than those obtained by X-ray crystallography. Using this approach, we obtained structures of neurotensin 1 receptor bound to antagonist SR48692, μ-opioid receptor bound to alvimopan, apo somatostatin receptor 2 and histamine receptor 2 bound to famotidine. We expect this rapid, straightforward approach to facilitate the broad exploration of GPCR inactive states without the need for extensive engineering and crystallization.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurotensin receptor 1A [auth R]419Homo sapiensMutation(s): 0 
Gene Names: NTSR1NTRROPRK1OPRK
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens)
Explore P41145 
Go to UniProtKB:  P41145
PHAROS:  P41145
GTEx:  ENSG00000082556 
Find proteins for P30989 (Homo sapiens)
Explore P30989 
Go to UniProtKB:  P30989
PHAROS:  P30989
GTEx:  ENSG00000101188 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41145P30989
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 6B [auth D]133Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q6Q (Subject of Investigation/LOI)
Query on Q6Q

Download Ideal Coordinates CCD File 
C [auth R]2-[[1-(7-chloranylquinolin-4-yl)-5-(2,6-dimethoxyphenyl)pyrazol-3-yl]carbonylamino]adamantane-2-carboxylic acid
C32 H31 Cl N4 O5
DYLJVOXRWLXDIG-LWXMPVTCSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth R]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Q6Q BindingDB:  7UL2 Kd: 8.9 (nM) from 1 assay(s)
IC50: min: 0.99, max: 82 (nM) from 2 assay(s)
EC50: 3.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The G. Harold and Leila Y. Mathers FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2022-12-28
    Changes: Database references
  • Version 1.4: 2024-09-25
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.6: 2024-11-06
    Changes: Data collection, Source and taxonomy