6LI2

Crystal structure of GPR52 ligand free form with rubredoxin fusion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of ligand recognition and self-activation of orphan GPR52.

Lin, X.Li, M.Wang, N.Wu, Y.Luo, Z.Guo, S.Han, G.W.Li, S.Yue, Y.Wei, X.Xie, X.Chen, Y.Zhao, S.Wu, J.Lei, M.Xu, F.

(2020) Nature 579: 152-157

  • DOI: https://doi.org/10.1038/s41586-020-2019-0
  • Primary Citation of Related Structures:  
    6LI0, 6LI1, 6LI2, 6LI3

  • PubMed Abstract: 

    GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders 1,2 . Pathological malfunction of GPR52 signalling occurs primarily through the heterotrimeric G s protein 2 , but it is unclear how GPR52 and G s couple for signal transduction and whether a native ligand or other activating input is required. Here we present the high-resolution structures of human GPR52 in three states: a ligand-free state, a G s -coupled self-activation state and a potential allosteric ligand-bound state. Together, our structures reveal that extracellular loop 2 occupies the orthosteric binding pocket and operates as a built-in agonist, conferring an intrinsically high level of basal activity to GPR52 3 . A fully active state is achieved when G s is coupled to GPR52 in the absence of an external agonist. The receptor also features a side pocket for ligand binding. These insights into the structure and function of GPR52 could improve our understanding of other self-activated GPCRs, enable the identification of endogenous and tool ligands, and guide drug discovery efforts that target GPR52.


  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera of G-protein coupled receptor 52 and Rubredoxin372Homo sapiensClostridium pasteurianumMutation(s): 5 
Gene Names: GPR52
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T5 (Homo sapiens)
Explore Q9Y2T5 
Go to UniProtKB:  Q9Y2T5
PHAROS:  Q9Y2T5
GTEx:  ENSG00000203737 
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Y2T5P00268
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
N [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.223α = 90
b = 113.229β = 90
c = 138.615γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description