6L53 | pdb_00006l53

Structure of SMG1

• PDB DOI: https://doi.org/10.2210/pdb6L53/pdb
• EM Map EMD-0836: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-10-22 Released: 2020-04-15 
• Deposition Author(s): Xu, Y., Qi, Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 31729466 
• DOI: https://doi.org/10.1038/s41422-019-0255-3
• Primary Citation 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.

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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.
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. [e-mail].
Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. [e-mail].
Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. [e-mail].
CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy, gel filtration, equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 410.97 kDa 
• Atom Count: 13,991 
• Modeled Residue Count: 1,935 
• Deposited Residue Count: 3,661 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase SMG1	A	3,661	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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