8YUT

Cryo-EM structure of the amthamine-bound H2R-Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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) : 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(s) subunit alpha isoforms short378Homo sapiensMutation(s): 0 
Gene Names: GNAS
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1356Homo 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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UniProt GroupP62873
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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
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Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody-35D [auth N]128synthetic constructMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H2 receptorE [auth R]411Homo sapiensMutation(s): 0 
Gene Names: HRH2
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Find proteins for P25021 (Homo sapiens)
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PHAROS:  P25021
GTEx:  ENSG00000113749 
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UniProt GroupP25021
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
A1D67 (Subject of Investigation/LOI)
Query on A1D67

Download Ideal Coordinates CCD File 
F [auth R]5-(2-azanylethyl)-4-methyl-1,3-thiazol-2-amine
C6 H11 N3 S
LHVRFUVVRXGZPV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19

Structure Validation

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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