5LTA

Crystal structure of the Prp43-ADP-BeF3-U7-RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.621 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.

Tauchert, M.J.Fourmann, J.B.Luhrmann, R.Ficner, R.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.21510
  • Primary Citation of Related Structures:  5LTJ, 5LTK

  • PubMed Abstract: 
  • The DEAH-box helicase Prp43 is a key player in pre-mRNA splicing as well as the maturation of rRNAs. The exact modus operandi of Prp43 and of all other spliceosomal DEAH-box RNA helicases is still elusive. Here, we report crystal structures of Prp43 ...

    The DEAH-box helicase Prp43 is a key player in pre-mRNA splicing as well as the maturation of rRNAs. The exact modus operandi of Prp43 and of all other spliceosomal DEAH-box RNA helicases is still elusive. Here, we report crystal structures of Prp43 complexes in different functional states and the analysis of structure-based mutants providing insights into the unwinding and loading mechanism of RNAs. The Prp43•ATP-analog•RNA complex shows the localization of the RNA inside a tunnel formed by the two RecA-like and C-terminal domains. In the ATP-bound state this tunnel can be transformed into a groove prone for RNA binding by large rearrangements of the C-terminal domains. Several conformational changes between the ATP- and ADP-bound states explain the coupling of ATP hydrolysis to RNA translocation, mainly mediated by a β-turn of the RecA1 domain containing the newly identified RF motif. This mechanism is clearly different to those of other RNA helicases.


    Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
A
714Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)N/A
Find proteins for G0RY84 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY84
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')E16synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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Download CCD File 
A
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.621 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.392α = 90.00
b = 106.392β = 90.00
c = 356.698γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
German Research FoundationGermanySFB860

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Data collection