4N48

Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein in complex with capped RNA fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation.

Smietanski, M.Werner, M.Purta, E.Kaminska, K.H.Stepinski, J.Darzynkiewicz, E.Nowotny, M.Bujnicki, J.M.

(2014) Nat Commun 5: 3004-3004

  • DOI: https://doi.org/10.1038/ncomms4004
  • Primary Citation of Related Structures:  
    4N48, 4N49, 4N4A

  • PubMed Abstract: 

    The 5' cap of human messenger RNA contains 2'-O-methylation of the first and often second transcribed nucleotide that is important for its processing, translation and stability. Human enzymes that methylate these nucleotides, termed CMTr1 and CMTr2, respectively, have recently been identified. However, the structures of these enzymes and their mechanisms of action remain unknown. In the present study, we solve the crystal structures of the active CMTr1 catalytic domain in complex with a methyl group donor and a capped oligoribonucleotide, thereby revealing the mechanism of specific recognition of capped RNA. This mechanism differs significantly from viral enzymes, thus providing a framework for their specific targeting. Based on the crystal structure of CMTr1, a comparative model of the CMTr2 catalytic domain is generated. This model, together with mutational analysis, leads to the identification of residues involved in RNA and methyl group donor binding.


  • Organizational Affiliation

    1] Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. ks. Trojdena 4, PL-02-109 Warsaw, Poland [2] Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, ul. ks. Trojdena 4, PL-02-109 Warsaw, Poland.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
A, B
428Homo sapiensMutation(s): 0 
Gene Names: FTSJD2KIAA0082MTR1
EC: 2.1.1.57
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N1G2 (Homo sapiens)
Explore Q8N1G2 
Go to UniProtKB:  Q8N1G2
PHAROS:  Q8N1G2
GTEx:  ENSG00000137200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N1G2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
capped RNAC [auth D],
D [auth G]
4N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.209α = 90.23
b = 60.038β = 97.83
c = 87.045γ = 116.25
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description