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 8JRU

Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Tail engagement of arrestin at the glucagon receptor.

Chen, K.Zhang, C.Lin, S.Yan, X.Cai, H.Yi, C.Ma, L.Chu, X.Liu, Y.Zhu, Y.Han, S.Zhao, Q.Wu, B.

(2023) Nature 620: 904-910

  • DOI: https://doi.org/10.1038/s41586-023-06420-x
  • Primary Citation of Related Structures:  
    8JRU, 8JRV

  • PubMed Abstract: 

    Arrestins have pivotal roles in regulating G protein-coupled receptor (GPCR) signalling by desensitizing G protein activation and mediating receptor internalization 1,2 . It has been proposed that the arrestin binds to the receptor in two different conformations, 'tail' and 'core', which were suggested to govern distinct processes of receptor signalling and trafficking 3,4 . However, little structural information is available for the tail engagement of the arrestins. Here we report two structures of the glucagon receptor (GCGR) bound to β-arrestin 1 (βarr1) in glucagon-bound and ligand-free states. These structures reveal a receptor tail-engaged binding mode of βarr1 with many unique features, to our knowledge, not previously observed. Helix VIII, instead of the receptor core, has a major role in accommodating βarr1 by forming extensive interactions with the central crest of βarr1. The tail-binding pose is further defined by a close proximity between the βarr1 C-edge and the receptor helical bundle, and stabilized by a phosphoinositide derivative that bridges βarr1 with helices I and VIII of GCGR. Lacking any contact with the arrestin, the receptor core is in an inactive state and loosely binds to glucagon. Further functional studies suggest that the tail conformation of GCGR-βarr governs βarr recruitment at the plasma membrane and endocytosis of GCGR, and provides a molecular basis for the receptor forming a super-complex simultaneously with G protein and βarr to promote sustained signalling within endosomes. These findings extend our knowledge about the arrestin-mediated modulation of GPCR functionalities.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, 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
HA signal peptide,HPC4 purification tag,Glucagon receptor,C-terminal tail of Vasopressin V2 receptorA [auth R]478Influenza A virus (A/Victoria/3/1975(H3N2))Homo sapiensMutation(s): 0 
Gene Names: HAPROCGCGRAVPR2ADHRDIRDIR3V2R
EC: 3.4.21.69
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P03435 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Explore P03435 
Go to UniProtKB:  P03435
Find proteins for P04070 (Homo sapiens)
Explore P04070 
Go to UniProtKB:  P04070
PHAROS:  P04070
GTEx:  ENSG00000115718 
Find proteins for P47871 (Homo sapiens)
Explore P47871 
Go to UniProtKB:  P47871
PHAROS:  P47871
GTEx:  ENSG00000215644 
Find proteins for P30518 (Homo sapiens)
Explore P30518 
Go to UniProtKB:  P30518
PHAROS:  P30518
GTEx:  ENSG00000126895 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP47871P03435P30518P04070
Sequence AnnotationsExpand
  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin 1 and single-chain fragment variable 30 (scFv30)B [auth A],
C [auth H],
D [auth L]
627Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17870 (Bos taurus)
Explore P17870 
Go to UniProtKB:  P17870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17870
Sequence AnnotationsExpand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 32E [auth B]126Escherichia phage EcSzw-2Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO (Subject of Investigation/LOI)
Query on PIO

Download Ideal Coordinates CCD File 
F [auth A][(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary