2VUQ

Crystal structure of a human tRNAGly acceptor stem microhelix (derived from the gene sequence DG9990) at 1.18 Angstroem resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Human Trnagly Microhelix Isoacceptor G9990 at 1.18 A Resolution

Eichert, A.Perbandt, M.Schreiber, A.Fuerste, J.P.Betzel, C.Erdmann, V.A.Foerster, C.

(2009) Biochem Biophys Res Commun 380: 503

  • DOI: 10.1016/j.bbrc.2009.01.127
  • Primary Citation of Related Structures:  
    2VUQ

  • PubMed Abstract: 
  • The tRNA(Gly)/Glycyl-tRNA synthetase system belongs to the so called 'class II' in which tRNA identity elements consist of relative few and simple motifs, as compared to 'class I' where the tRNA determinants are more complicated and spread over different parts of the tRNA, mostly including the anticodon ...

    The tRNA(Gly)/Glycyl-tRNA synthetase system belongs to the so called 'class II' in which tRNA identity elements consist of relative few and simple motifs, as compared to 'class I' where the tRNA determinants are more complicated and spread over different parts of the tRNA, mostly including the anticodon. The determinants from 'class II' although, are located in the aminoacyl stem and sometimes include the discriminator base. There exist predominant structure differences for the Glycyl-tRNA-synthetases and for the tRNA(Gly) identity elements comparing eucaryotic/archaebacterial and eubacterial systems. We focus on comparative X-ray structure analysis of tRNA(Gly) acceptor stem microhelices from different organisms. Here, we report the X-ray structure of the human tRNA(Gly) microhelix isoacceptor G9990 at 1.18A resolution. Superposition experiments to another human tRNA(Gly) microhelix and a detailed comparison of the RNA hydration patterns show a great number of water molecules with identical positions in both RNAs. This is the first structure comparison of hydration layers from two isoacceptor tRNA microhelices with a naturally occurring base pair exchange.


    Organizational Affiliation

    Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*AP*UP*UP*GP*GP)-3'A 7Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*CP*CP*AP*AP*UP*GP*CP)-3'B 7Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.318α = 90
b = 37.613β = 112.6
c = 30.465γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other