7YDH

Cryo EM structure of CD97/miniG13 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Structural basis of CD97 activation and G-protein coupling.

Wang, N.Qian, Y.Xia, R.Zhu, X.Xiong, Y.Zhang, A.Guo, C.He, Y.

(2023) Cell Chem Biol 30: 1343-1353.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2023.08.003
  • Primary Citation of Related Structures:  
    7YDH, 7YDM, 7YDP

  • PubMed Abstract: 

    CD97 (ADGRE5) is an adhesion G protein-coupled receptor (aGPCR) which plays crucial roles in immune system and cancer. However, the mechanism of CD97 activation and the determinant of G 13 coupling selectivity remain unknown. Here, we present the cryo-electron microscopy structures of human CD97 in complex with G 13 , G q , and G s . Our structures reveal the stalk peptide recognition mode of CD97, adding missing information of the current tethered-peptide activation model of aGPCRs. For instance, a revised "FXφφφ" motif and a framework of conserved aromatic residues in the ligand-binding pocket. Importantly, structural comparisons of G 13 , G q , and G s engagements of CD97 reveal key determinants of G 13 coupling selectivity, where a deep insertion of the α helix 5 and a closer contact with the transmembrane helix 6, 5, and 3 dictate coupling preferences. Taken together, our structural study of CD97 provides a framework for understanding CD97 signaling and the G 13 coupling selectivity.


  • Organizational Affiliation

    Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G protein subunit 13 (Gi2-mini-G13 chimera)230Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14344 (Homo sapiens)
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Go to UniProtKB:  Q14344
PHAROS:  Q14344
GTEx:  ENSG00000120063 
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UniProt GroupQ14344
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16C [auth E]247Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Adhesion G protein-coupled receptor E5 subunit betaE [auth R]307Homo sapiensMutation(s): 0 
Gene Names: ADGRE5CD97
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48960 (Homo sapiens)
Explore P48960 
Go to UniProtKB:  P48960
PHAROS:  P48960
GTEx:  ENSG00000123146 
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UniProt GroupP48960
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070048

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-27
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Database references
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary