8JD0

Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of NAM563


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into dimerization and activation of the mGlu2-mGlu3 and mGlu2-mGlu4 heterodimers.

Wang, X.Wang, M.Xu, T.Feng, Y.Shao, Q.Han, S.Chu, X.Xu, Y.Lin, S.Zhao, Q.Wu, B.

(2023) Cell Res 33: 762-774

  • DOI: https://doi.org/10.1038/s41422-023-00830-2
  • Primary Citation of Related Structures:  
    8JCU, 8JCV, 8JCW, 8JCX, 8JCY, 8JCZ, 8JD0, 8JD1, 8JD2, 8JD3, 8JD4, 8JD5, 8JD6

  • PubMed Abstract: 

    Heterodimerization of the metabotropic glutamate receptors (mGlus) has shown importance in the functional modulation of the receptors and offers potential drug targets for treating central nervous system diseases. However, due to a lack of molecular details of the mGlu heterodimers, understanding of the mechanisms underlying mGlu heterodimerization and activation is limited. Here we report twelve cryo-electron microscopy (cryo-EM) structures of the mGlu2-mGlu3 and mGlu2-mGlu4 heterodimers in different conformational states, including inactive, intermediate inactive, intermediate active and fully active conformations. These structures provide a full picture of conformational rearrangement of mGlu2-mGlu3 upon activation. The Venus flytrap domains undergo a sequential conformational change, while the transmembrane domains exhibit a substantial rearrangement from an inactive, symmetric dimer with diverse dimerization patterns to an active, asymmetric dimer in a conserved dimerization mode. Combined with functional data, these structures reveal that stability of the inactive conformations of the subunits and the subunit-G protein interaction pattern are determinants of asymmetric signal transduction of the heterodimers. Furthermore, a novel binding site for two mGlu4 positive allosteric modulators was observed in the asymmetric dimer interfaces of the mGlu2-mGlu4 heterodimer and mGlu4 homodimer, and may serve as a drug recognition site. These findings greatly extend our knowledge about signal transduction of the mGlus.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1AA [auth 2]993Homo sapiensMutation(s): 0 
Gene Names: GRM2GPRC1BMGLUR2FKBP1AFKBP1FKBP12
EC: 5.2.1.8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14416 (Homo sapiens)
Explore Q14416 
Go to UniProtKB:  Q14416
PHAROS:  Q14416
GTEx:  ENSG00000164082 
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP62942Q14416
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P62942-1Q14416-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTORB [auth 3]993Homo sapiensMutation(s): 0 
Gene Names: GRM3GPRC1CMGLUR3MTOR
EC: 2.7.11.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14832 (Homo sapiens)
Explore Q14832 
Go to UniProtKB:  Q14832
PHAROS:  Q14832
GTEx:  ENSG00000198822 
Find proteins for A0A8V8TRG9 (Homo sapiens)
Explore A0A8V8TRG9 
Go to UniProtKB:  A0A8V8TRG9
GTEx:  ENSG00000198793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ14832A0A8V8TRG9
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q14832-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J9R (Subject of Investigation/LOI)
Query on J9R

Download Ideal Coordinates CCD File 
D [auth 2]4-(1-methylpyrazol-4-yl)-7-[[(2~{S})-2-(trifluoromethyl)morpholin-4-yl]methyl]quinoline-2-carboxamide
C20 H20 F3 N5 O2
PUIAIYDBFPDZPF-SFHVURJKSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
E [auth 2]
F [auth 2]
G [auth 2]
H [auth 2]
K [auth 3]
E [auth 2],
F [auth 2],
G [auth 2],
H [auth 2],
K [auth 3],
L [auth 3],
M [auth 3],
N [auth 3],
O [auth 3]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth 2],
J [auth 3]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU (Subject of Investigation/LOI)
Query on GLU

Download Ideal Coordinates CCD File 
I [auth 3]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31825010
National Science Foundation (NSF, China)China82121005

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary