9C3I | pdb_00009c3i

Rebuilt CNOT3/tRNA-LEU structure

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens, Oryctolagus cuniculus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-06-01 Released: 2024-12-04 
  • Deposition Author(s): Erzberger, J.P., Cruz, V.E.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8BHF


Literature

Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.

Zhu, X.Cruz, V.E.Zhang, H.Erzberger, J.P.Mendell, J.T.

(2024) Science 386: eadq8587-eadq8587

  • DOI: https://doi.org/10.1126/science.adq8587
  • Primary Citation of Related Structures:  
    9C3H, 9C3I

  • PubMed Abstract: 

    The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. We applied selective ribosome profiling to further investigate the determinants of CCR4-NOT recruitment to ribosomes in mammalian cells. This revealed that specific arginine codons in the P-site are strong signals for ribosomal recruitment of human CNOT3, a CCR4-NOT subunit. Cryo-electron microscopy and transfer RNA (tRNA) mutagenesis demonstrated that the D-arms of select arginine tRNAs interact with CNOT3 and promote its recruitment whereas other tRNA D-arms sterically clash with CNOT3. These effects link codon content to mRNA stability. Thus, in addition to their canonical decoding function, tRNAs directly engage regulatory complexes during translation, a mechanism we term P-site tRNA-mediated mRNA decay.


  • Organizational Affiliation
    • Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 3A [auth S]609Homo sapiensMutation(s): 0 
Gene Names: CNOT3KIAA0691LENG2NOT3
UniProt & NIH Common Fund Data Resources
Find proteins for O75175 (Homo sapiens)
Explore O75175 
Go to UniProtKB:  O75175
PHAROS:  O75175
GTEx:  ENSG00000088038 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75175
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA Leu, UAA-1-1B [auth A]86Oryctolagus cuniculus
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA282036
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135617-01
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220309
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR150074
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170644
Welch FoundationUnited StatesI-1961
Welch FoundationUnited StatesI-1897

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release