5M0H | pdb_00005m0h

Crystal structure of the central flexible region of ASH1 mRNA E3-localization element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.240 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex.

Edelmann, F.T.Schlundt, A.Heym, R.G.Jenner, A.Niedner-Boblenz, A.Syed, M.I.Paillart, J.C.Stehle, R.Janowski, R.Sattler, M.Jansen, R.P.Niessing, D.

(2017) Nat Struct Mol Biol 24: 152-161

  • DOI: https://doi.org/10.1038/nsmb.3351
  • Primary Citation Related Structures: 
    5M0H, 5M0I, 5M0J

  • PubMed Abstract: 

    mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p. Although the RNA alone formed a flexible stem loop, She2p binding induced marked conformational changes. However, only joining by the unstructured She3p resulted in specific RNA recognition. The notable RNA rearrangements and joint action of a globular and an unfolded RNA-binding protein offer unprecedented insights into the step-wise maturation of an mRNA-transport complex.


  • Organizational Affiliation
    • Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 13.6 kDa 
  • Atom Count: 909 
  • Modeled Residue Count: 42 
  • Deposited Residue Count: 42 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
ASH1 E3 (42 nt-TL/TLR)42Saccharomyces cerevisiae
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.240 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.32α = 90
b = 64.32β = 90
c = 75.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-15
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description