1T0K

Joint X-ray and NMR Refinement of Yeast L30e-mRNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.269 

wwPDB Validation 3D Report Full Report



Literature

Joint X-Ray and NMR Refinement of the Yeast L30e-mRNA Complex

Chao, J.A.Williamson, J.R.

(2004) Structure 12: 1165-1176

  • DOI: 10.1016/j.str.2004.04.023
  • Primary Citation of Related Structures:  
    1T0K

  • PubMed Abstract: 
  • L30e, a Saccharomyces cervisiae ribosomal protein, regulates its own expression by binding to a purine-rich asymmetric internal loop located in both its pre-mRNA and mature mRNA. A crystal structure of an MBP-L30e fusion protein in complex with an RN ...

    L30e, a Saccharomyces cervisiae ribosomal protein, regulates its own expression by binding to a purine-rich asymmetric internal loop located in both its pre-mRNA and mature mRNA. A crystal structure of an MBP-L30e fusion protein in complex with an RNA containing the pre-mRNA regulatory site was solved at 3.24 A. Interestingly, the structure of the RNA differed from that observed in a previously determined NMR structure of the complex. Analysis of the NMR data led to the identification of a single imino proton resonance in the internal loop that had been incorrectly assigned and was principally responsible for the erroneous RNA structure. A structure refinement was performed using both the X-ray diffraction data and the NMR-derived distance and angle restraints. The joint NMR and X-ray refinement resulted in improved stereochemistry and lower crystallographic R factors. The RNA internal loop of the MBP-L30e-mRNA complex adopts the canonical K-turn fold.


    Organizational Affiliation

    Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinA381Escherichia coliMutation(s): 0 
Gene Names: malEb4034Z5632ECS5017
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30B105Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14120 
Go to UniProtKB:  P14120
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*AP*CP*CP*GP*GP*AP*GP*UP*GP*UP*CP*C)-3'C13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-R(*G*GP*AP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*GP*UP*C)-3'D16N/A
      Oligosaccharides

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      Entity ID: 5
      MoleculeChainsChain Length2D Diagram Glycosylation
      alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
      E
      4 N/A
      Biologically Interesting Molecules (External Reference) 1 Unique
      Entity ID: 5
      IDChainsNameType/Class2D Diagram3D Interactions
      PRD_900010
      Query on PRD_900010
      Ealpha-maltotetraoseOligosaccharide /  Substrate analog

      --

      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.24 Å
      • R-Value Free: 0.320 
      • R-Value Work: 0.261 
      • R-Value Observed: 0.269 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 136.006α = 90
      b = 136.006β = 90
      c = 123.813γ = 90
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      SCALAdata scaling
      AMoREphasing
      CNSrefinement
      CCP4data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-07-20
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 2.0: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary