8IKL

Cryo-EM structure of the CD97-G13 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.33 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

Conformational transitions and activation of the adhesion receptor CD97.

Mao, C.Zhao, R.J.Dong, Y.J.Gao, M.Chen, L.N.Zhang, C.Xiao, P.Guo, J.Qin, J.Shen, D.D.Ji, S.Y.Zang, S.K.Zhang, H.Wang, W.W.Shen, Q.Sun, J.P.Zhang, Y.

(2024) Mol Cell 84: 570-583.e7

  • DOI: https://doi.org/10.1016/j.molcel.2023.12.020
  • Primary Citation of Related Structures:  
    8IKJ, 8IKL

  • PubMed Abstract: 

    Adhesion G protein-coupled receptors (aGPCRs) are evolutionarily ancient receptors involved in a variety of physiological and pathophysiological processes. Modulators of aGPCR, particularly antagonists, hold therapeutic promise for diseases like cancer and immune and neurological disorders. Hindered by the inactive state structural information, our understanding of antagonist development and aGPCR activation faces challenges. Here, we report the cryo-electron microscopy structures of human CD97, a prototypical aGPCR that plays crucial roles in immune system, in its inactive apo and G13-bound fully active states. Compared with other family GPCRs, CD97 adopts a compact inactive conformation with a constrained ligand pocket. Activation induces significant conformational changes for both extracellular and intracellular sides, creating larger cavities for Stachel sequence binding and G13 engagement. Integrated with functional and metadynamics analyses, our study provides significant mechanistic insights into the activation and signaling of aGPCRs, paving the way for future drug discovery efforts.


  • Organizational Affiliation

    Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China. Electronic address: maochunyou@zju.edu.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adhesion G protein-coupled receptor E5A [auth R]278Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48960
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(13) subunit alpha isoforms shortB [auth A]229Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P08754 (Homo sapiens)
Explore P08754 
Go to UniProtKB:  P08754
PHAROS:  P08754
GTEx:  ENSG00000065135 
Find proteins for Q14344 (Homo sapiens)
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PHAROS:  Q14344
GTEx:  ENSG00000120063 
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UniProt GroupsP08754Q14344
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]338Homo 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth Y]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary