9II2 | pdb_00009ii2

Cryo-EM Structure of the 2:2 Complex of mGlu3 and beta-arrestin1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis of beta-arrestin coupling to the metabotropic glutamate receptor mGlu3.

Wen, T.Du, M.Lu, Y.Jia, N.Lu, X.Liu, N.Chang, S.Zhang, X.Shen, Y.Yang, X.

(2025) Nat Chem Biol 21: 1262-1269

  • DOI: https://doi.org/10.1038/s41589-025-01858-8
  • Primary Citation of Related Structures:  
    9II2, 9II3

  • PubMed Abstract: 

    β-Arrestins (βarrs) mediate the desensitization and internalization of activated G-protein-coupled receptors (GPCRs). The molecular mechanism by which dimeric family C GPCR members recruit arrestins remains elusive. Here we report two structures of metabotropic glutamate receptor subtype 3 (mGlu3) coupled to βarr1, with stoichiometries of 2:1 and 2:2. The L-glutamate-bound mGlu3 dimer adopts an inactive state, with both Venus flytrap domains closed, engaging βarr1 either asymmetrically or symmetrically. The transmembrane domain of the mGlu3 protomer interacts with βarr1 through a binding pocket formed by three intracellular loops and an ordered C-terminal region. Three phosphorylation sites (pS857, pS859 and pT860) on the C-terminal tail of mGlu3 engage the N domain of βarr1. βarr1 stabilizes mGlu3 in an inactive conformation, characterized by a TM3/TM4-TM3/TM4 dimeric interface, previously observed in the negative allosteric modulator-bound structure of mGlu3. Our findings provide important insights into βarr-mediated inactivation of family C GPCRs.


  • Organizational Affiliation
    • State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 3A [auth R],
D [auth B]
879Homo sapiensMutation(s): 0 
Gene Names: GRM3GPRC1CMGLUR3
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14832
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q14832-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-1B [auth A],
E [auth C]
418Homo sapiensMutation(s): 0 
Gene Names: ARRB1ARR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens)
Explore P49407 
Go to UniProtKB:  P49407
PHAROS:  P49407
GTEx:  ENSG00000137486 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49407
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv30C [auth S],
F [auth D]
251Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E],
H [auth F]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
J [auth R]
K [auth R]
L [auth R]
N [auth B]
O [auth B]
J [auth R],
K [auth R],
L [auth R],
N [auth B],
O [auth B],
P [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
I [auth R],
M [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth R],
D [auth B]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth R],
D [auth B]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection
  • Version 1.3: 2025-08-13
    Changes: Data collection, Database references