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 

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This is version 2.0 of the entry. See complete history


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 RNA containing the pre-mRNA regulatory site was solved at 3 ...

    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)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinC [auth A]381Escherichia coliMutation(s): 0 
Gene Names: malEb4034Z5632ECS5017
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
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UniProt GroupP0AEX9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30D [auth B]105Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14120 
Go to UniProtKB:  P14120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14120
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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'A [auth C]13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*G*GP*AP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*GP*UP*C)-3'B [auth D]16N/A
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseE 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G87171PZ
GlyCosmos:  G87171PZ
GlyGen:  G87171PZ
Biologically Interesting Molecules (External Reference) 1 Unique
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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