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 1.2 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: 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 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. conti@biochem.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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 SMG1A3,712Homo sapiensMutation(s): 1 
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
Entity Groups  
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UniProt GroupQ96Q15
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SMG8B991Homo 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
Entity Groups  
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UniProt GroupQ8ND04
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SMG9C520Homo 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
Entity Groups  
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UniProt GroupQ9H0W8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
D [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
ATP
Query on ATP

Download Ideal Coordinates CCD File 
E [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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