8YUV

Cryo-EM structure of the immepip-bound H3R-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Molecular Determinant Underlying Selective Coupling of Primary G-Protein by Class A GPCRs.

Shen, Q.Tang, X.Wen, X.Cheng, S.Xiao, P.Zang, S.K.Shen, D.D.Jiang, L.Zheng, Y.Zhang, H.Xu, H.Mao, C.Zhang, M.Hu, W.Sun, J.P.Zhang, Y.Chen, Z.

(2024) Adv Sci (Weinh) 11: e2310120-e2310120

  • DOI: https://doi.org/10.1002/advs.202310120
  • Primary Citation of Related Structures:  
    8YUT, 8YUU, 8YUV

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs) transmit downstream signals predominantly via G-protein pathways. However, the conformational basis of selective coupling of primary G-protein remains elusive. Histamine receptors H 2 R and H 3 R couple with G s - or G i -proteins respectively. Here, three cryo-EM structures of H 2 R-G s and H 3 R-G i complexes are presented at a global resolution of 2.6-2.7 Å. These structures reveal the unique binding pose for endogenous histamine in H 3 R, wherein the amino group interacts with E206 5.46 of H 3 R instead of the conserved D114 3.32 of other aminergic receptors. Furthermore, comparative analysis of the H 2 R-G s and H 3 R-G i complexes reveals that the structural geometry of TM5/TM6 determines the primary G-protein selectivity in histamine receptors. Machine learning (ML)-based structuromic profiling and functional analysis of class A GPCR-G-protein complexes illustrate that TM5 length, TM5 tilt, and TM6 outward movement are key determinants of the G s and G i/o selectivity among the whole Class A family. Collectively, the findings uncover the common structural geometry within class A GPCRs that determines the primary G s - and G i/o -coupling selectivity.


  • Organizational Affiliation

    Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu Laboratory, Hangzhou, 310058, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1358Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth S]269Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H3 receptorE [auth R]461Homo sapiensMutation(s): 0 
Gene Names: HRH3GPCR97
Membrane Entity: Yes 
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Find proteins for Q9Y5N1 (Homo sapiens)
Explore Q9Y5N1 
Go to UniProtKB:  Q9Y5N1
PHAROS:  Q9Y5N1
GTEx:  ENSG00000101180 
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UniProt GroupQ9Y5N1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2019YFA050880

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary