7PW4

Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8.

Langer, L.M.Bonneau, F.Gat, Y.Conti, E.

(2021) Elife 10

  • DOI: 10.7554/eLife.72353
  • Primary Citation of Related Structures:  
    7PW4, 7PW5, 7PW6, 7PW7, 7PW8, 7PW9

  • PubMed Abstract: 
  • The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain ...

    The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain. However, the molecular basis for this complex regulatory network has remained elusive. Here, we present cryo-electron microscopy reconstructions of human SMG1-9 and SMG1-8-9 complexes bound to either a SMG1 inhibitor or a non-hydrolyzable ATP analog at overall resolutions ranging from 2.8 to 3.6 Å. These structures reveal the basis with which a small molecule inhibitor preferentially targets SMG1 over other PIKKs. By comparison with our previously reported substrate-bound structure (Langer et al.,2020), we show that the SMG1 insertion domain can exert an autoinhibitory function by directly blocking the substrate-binding path as well as overall access to the SMG1 kinase active site. Together with biochemical analysis, our data indicate that SMG1 autoinhibition is stabilized by the presence of SMG8. Our results explain the specific inhibition of SMG1 by an ATP-competitive small molecule, provide insights into regulation of its kinase activity within the NMD pathway, and expand the understanding of PIKK regulatory mechanisms in general.


    Organizational Affiliation

    Max Planck Institute of Biochemistry, Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1A3,657Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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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  • Reference Sequence
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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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
D [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
88C (Subject of Investigation/LOI)
Query on 88C

Download Ideal Coordinates CCD File 
E [auth A]1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea
C27 H28 Cl N7 O3 S
RZFJBSIAXYEPBX-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

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

Download Ideal Coordinates CCD File 
G [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release