6L54

Structure of SMG189


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of SMG1-SMG8-SMG9 complex.

Zhu, L.Li, L.Qi, Y.Yu, Z.Xu, Y.

(2019) Cell Res 29: 1027-1034

  • DOI: https://doi.org/10.1038/s41422-019-0255-3
  • Primary Citation of Related Structures:  
    6L53, 6L54

  • PubMed Abstract: 

    Nonsense-mediated mRNA decay (NMD) targets premature stop codon (PTC)-containing mRNAs for rapid degradation, and is essential for mammalian embryonic development, brain development and modulation of the stress response. The key event in NMD is the SMG1-mediated phosphorylation of an RNA helicase UPF1 and SMG1 kinase activity is inhibited by SMG8 and SMG9 in an unknown mechanism. Here, we determined the cryo-EM structures of human SMG1 at 3.6 Å resolution and the SMG1-SMG8-SMG9 complex at 3.4 Å resolution, respectively. SMG8 has a C-terminal kinase inhibitory domain (KID), which covers the catalytic pocket and inhibits the kinase activity of SMG1. Structural analyses suggest that GTP hydrolysis of SMG9 would lead to a dramatic conformational change of SMG8-SMG9 and the KID would move away from the inhibitory position to restore SMG1 kinase activity. Thus, our structural and biochemical analyses provide a mechanistic understanding of SMG1-SMG8-SMG9 complex assembly and the regulatory mechanism of SMG1 kinase activity.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College of Fudan University, Shanghai, 200032, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase SMG13,661Homo sapiensMutation(s): 0 
Gene Names: SMG1ATXKIAA0421LIP
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96Q15 (Homo sapiens)
Explore Q96Q15 
Go to UniProtKB:  Q96Q15
PHAROS:  Q96Q15
GTEx:  ENSG00000157106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96Q15
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SMG8991Homo sapiensMutation(s): 0 
Gene Names: SMG8ABC2C17orf71
UniProt & NIH Common Fund Data Resources
Find proteins for Q8ND04 (Homo sapiens)
Explore Q8ND04 
Go to UniProtKB:  Q8ND04
PHAROS:  Q8ND04
GTEx:  ENSG00000167447 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ND04
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SMG9520Homo sapiensMutation(s): 0 
Gene Names: SMG9C19orf61
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0W8 (Homo sapiens)
Explore Q9H0W8 
Go to UniProtKB:  Q9H0W8
PHAROS:  Q9H0W8
GTEx:  ENSG00000105771 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0W8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2020-04-15 
  • Deposition Author(s): Xu, Y., Qi, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references