8ITL

Cryo-EM structure of GIPR splice variant 1 (SV1) in complex with Gs protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular basis of signal transduction mediated by the human GIPR splice variants.

Zhao, F.Hang, K.Zhou, Q.Shao, L.Li, H.Li, W.Lin, S.Dai, A.Cai, X.Liu, Y.Xu, Y.Feng, W.Yang, D.Wang, M.W.

(2023) Proc Natl Acad Sci U S A 120: e2306145120-e2306145120

  • DOI: https://doi.org/10.1073/pnas.2306145120
  • Primary Citation of Related Structures:  
    8ITL, 8ITM

  • PubMed Abstract: 

    Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a potential drug target for metabolic disorders. It works with glucagon-like peptide-1 receptor and glucagon receptor in humans to maintain glucose homeostasis. Unlike the other two receptors, GIPR has at least 13 reported splice variants (SVs), more than half of which have sequence variations at either C or N terminus. To explore their roles in endogenous peptide-mediated GIPR signaling, we determined the cryoelectron microscopy (cryo-EM) structures of the two N terminus-altered SVs (referred as GIPR-202 and GIPR-209 in the Ensembl database, SV1 and SV2 here, respectively) and investigated the outcome of coexpressing each of them in question with GIPR in HEK293T cells with respect to ligand binding, receptor expression, cAMP (adenosine 3,5-cyclic monophosphate) accumulation, β-arrestin recruitment, and cell surface localization. It was found that while both N terminus-altered SVs of GIPR neither bound to the hormone nor elicited signal transduction per se, they suppressed ligand binding and cAMP accumulation of GIPR. Meanwhile, SV1 reduced GIPR-mediated β-arrestin 2 responses. The cryo-EM structures of SV1 and SV2 showed that they reorganized the extracellular halves of transmembrane helices 1, 6, and 7 and extracellular loops 2 and 3 to adopt a ligand-binding pocket-occupied conformation, thereby losing binding ability to the peptide. The results suggest a form of signal bias that is constitutive and ligand-independent, thus expanding our knowledge of biased signaling beyond pharmacological manipulation (i.e., ligand specific) as well as constitutive and ligand-independent (e.g., SV1 of the growth hormone-releasing hormone receptor).


  • Organizational Affiliation

    The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gastric inhibitory polypeptide receptorA [auth R]364Homo sapiensMutation(s): 1 
Gene Names: GIPR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48546 (Homo sapiens)
Explore P48546 
Go to UniProtKB:  P48546
PHAROS:  P48546
GTEx:  ENSG00000010310 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48546
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortB [auth A]394Bos taurusMutation(s): 8 
Gene Names: GNASGNAS1
Membrane Entity: Yes 
UniProt
Find proteins for P04896 (Bos taurus)
Explore P04896 
Go to UniProtKB:  P04896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04896
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]371Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54311
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63212
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35E [auth N]128synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81872915
National Natural Science Foundation of China (NSFC)China82073904
National Natural Science Foundation of China (NSFC)China82121005
National Natural Science Foundation of China (NSFC)China81973373
National Natural Science Foundation of China (NSFC)China21704064
National Natural Science Foundation of China (NSFC)China82204474

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release