5M0I

Crystal structure of the nuclear complex with She2p and the ASH1 mRNA E3-localization element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SWI5-dependent HO expression protein 2A [auth D],
B [auth C],
C [auth B],
D [auth A]
246Saccharomyces cerevisiae RM11-1aMutation(s): 4 
Gene Names: SHE2SCRG_03894
UniProt
Find proteins for P36068 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36068 
Go to UniProtKB:  P36068
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36068
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SWI5-dependent HO expression protein 3G [auth H],
H [auth J],
I
24Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SHE3YBR130CYBR1005
UniProt
Find proteins for P38272 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38272 
Go to UniProtKB:  P38272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38272
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
ASH1-E3 element, RNA (28-MER)
E, F
28Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth D]
K [auth D]
N [auth C]
O [auth C]
P [auth C]
J [auth D],
K [auth D],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth B],
X [auth A],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
FA [auth F]
M [auth D]
AA [auth E],
BA [auth E],
CA [auth E],
FA [auth F],
M [auth D],
W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth F]
EA [auth F]
L [auth D]
T [auth C]
V [auth B]
DA [auth F],
EA [auth F],
L [auth D],
T [auth C],
V [auth B],
Y [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.52α = 90
b = 58.34β = 126.98
c = 146.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

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, Derived calculations, Refinement description