6SYT

Structure of the SMG1-SMG8-SMG9 complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

InsP6binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.

Gat, Y., Schuller, J.M., Lingaraju, M., Weyher, E., Bonneau, F., Strauss, M., Murray, P.J., Conti, E.

(2019) Nat Struct Mol Biol 26: 1089-1093

  • DOI: https://doi.org/10.1038/s41594-019-0342-7
  • Primary Citation of Related Structures:  
    6SYT

  • PubMed Abstract: 

    We report the 3.45-Å resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance. Structural and MS analyses reveal the presence of inositol hexaphosphate (InsP 6 ) in the SMG1 kinase. We show that the InsP 6 -binding site is conserved in mammalian target of rapamycin (mTOR) and potentially other PIKK members, and that it is required for optimal in vitro phosphorylation of both SMG1 and mTOR substrates.

    • Organizational Affiliation: 

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG13,712Homo sapiensMutation(s): 1 
Gene Names: SMG1, ATX, KIAA0421, LIP
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: SMG8, ABC2, C17orf71
UniProt & NIH Common Fund Data Resources
Find proteins for Q8ND04 (Homo sapiens)
Explore Q8ND04 
Go to UniProtKB:  Q8ND04
PHAROS:  Q8ND04
GTEx:  ENSG00000167447 
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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: SMG9, C19orf61
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2020-10-07
    Changes: Structure summary
  • Version 1.3: 2024-05-22
    Changes: Data collection, Database references