6LI0

Crystal structure of GPR52 in complex with agonist c17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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 Flavodoxin468Homo sapiensNitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 8 
Gene Names: GPR52DVU_2680
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 P00323 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Y2T5P00323
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EN6 (Subject of Investigation/LOI)
Query on EN6

Download Ideal Coordinates CCD File 
B [auth A]N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide
C24 H22 F3 N3 O3 S
VJMRKWPMFQGIPI-UHFFFAOYSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
O [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
K [auth A]
W [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
K [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EN6 BindingDB:  6LI0 EC50: 21 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.97α = 90
b = 88.36β = 90
c = 156.28γ = 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 (NSF, 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