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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein
A
381Escherichia coli (strain K12)Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
B
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL30
Go to UniProtKB:  P14120
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*AP*CP*CP*GP*GP*AP*GP*UP*GP*UP*CP*C)-3'C13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*G*GP*AP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*GP*UP*C)-3'D16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTT
Query on MTT

Download SDF File 
Download CCD File 
A
MALTOTETRAOSE
C24 H42 O21
LUEWUZLMQUOBSB-ZLBHSGTGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.261 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 136.006α = 90.00
b = 136.006β = 90.00
c = 123.813γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance