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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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 Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1A, B428Homo sapiensMutation(s): 0 
Gene Names: FTSJD2KIAA0082MTR1CMTR1
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
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    capped RNAC [auth D], D [auth G]4N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MGT
    Query on MGT

    Download Ideal Coordinates CCD File 
    G [auth D], H [auth G]7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
    C11 H20 N5 O14 P3
    BUJQMJUTTBGELS-KQYNXXCUSA-N
     Ligand Interaction
    SAM
    Query on SAM

    Download Ideal Coordinates CCD File 
    E [auth A], F [auth B]S-ADENOSYLMETHIONINE
    C15 H22 N6 O5 S
    MEFKEPWMEQBLKI-FCKMPRQPSA-N
     Ligand Interaction
    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

    View Full Validation Report



    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