5AOR

Structure of MLE RNA ADP AlF4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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This is version 1.1 of the entry. See complete history


Literature

Structure of the RNA Helicase Mle Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling.

Prabu, J.R.Muller, M.Thomae, A.W.Schussler, S.Bonneau, F.Becker, P.B.Conti, E.

(2015) Mol Cell 60: 487

  • DOI: https://doi.org/10.1016/j.molcel.2015.10.011
  • Primary Citation of Related Structures:  
    5AOR

  • PubMed Abstract: 

    The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. We identified a stable MLE core comprising the DExH helicase module and two auxiliary domains: a dsRBD and an OB-like fold. MLEcore is an unusual DExH helicase that can unwind blunt-ended RNA duplexes and has specificity for uridine nucleotides. We determined the 2.1 Å resolution structure of MLEcore bound to a U10 RNA and ADP-AlF4. The OB-like and dsRBD folds bind the DExH module and contribute to form the entrance of the helicase channel. Four uridine nucleotides engage in base-specific interactions, rationalizing the conservation of uridine-rich sequences in critical roX substrates. roX2 binding is orchestrated by MLE's auxiliary domains, which is prerequisite for MLE localization to the male X chromosome. The structure visualizes a transition-state mimic of the reaction and suggests how eukaryotic DEAH/RHA helicases couple ATP hydrolysis to RNA translocation.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DOSAGE COMPENSATION REGULATOR
A, B
1,293Drosophila melanogasterMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P24785 (Drosophila melanogaster)
Explore P24785 
Go to UniProtKB:  P24785
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24785
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
C, D
11synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF
Query on ALF

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.373α = 90
b = 154.373β = 90
c = 198.194γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description