Structural and catalytic roles of human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report

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Structural and catalytic roles of the human 18SrRNA methyltransferases DIMT1 in ribosome assembly and translation.

Shen, H.Stoute, J.Liu, K.F.

(2020) J Biol Chem 295: 12058-12070

  • DOI: https://doi.org/10.1074/jbc.RA120.014236
  • Primary Citation of Related Structures:  
    6W6C, 6W6F

  • PubMed Abstract: 

    rRNA-modifying enzymes participate in ribosome assembly. However, whether the catalytic activities of these enzymes are important for the ribosome assembly and other cellular processes is not fully understood. Here, we report the crystal structure of WT human dimethyladenosine transferase 1 (DIMT1), an 18 S rRNA N 6,6 -dimethyladenosine (m 2 6,6 A) methyltransferase, and results obtained with a catalytically inactive DIMT1 variant. We found that DIMT1 +/- heterozygous HEK 293T cells have a significantly decreased 40S fraction and reduced protein synthesis but no major changes in m 2 6,6 A levels in 18 S rRNA. Expression of a catalytically inactive variant, DIMT1-E85A, in WT and DIMT1 +/- cells significantly decreased m 2 6,6 A levels in 18S rRNA, indicating a dominant-negative effect of this variant on m 2 6,6 A levels. However, expression of the DIMT1-E85A variant restored the defects in 40S levels. Of note, unlike WT DIMT1, DIMT1-E85A could not revert the defects in protein translation. We found that the differences between this variant and the WT enzyme extended to translation fidelity and gene expression patterns in DNA damage response pathways. These results suggest that the catalytic activity of DIMT1 is involved in protein translation and that the overall protein scaffold of DIMT1, regardless of the catalytic activity on m 2 6,6 A in 18 S rRNA, is essential for 40S assembly.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable dimethyladenosine transferase
A, B
313Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNQ2 (Homo sapiens)
Explore Q9UNQ2 
Go to UniProtKB:  Q9UNQ2
GTEx:  ENSG00000086189 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNQ2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.204α = 90
b = 96.504β = 90
c = 150.019γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM133721-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2020-09-02
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description