5LTJ | pdb_00005ltj

Crystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.199 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.7554/eLife.21510
  • Primary Citation Related Structures: 
    5LTA, 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 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.

Macromolecule Content 

  • Total Structure Weight: 83.34 kDa 
  • Atom Count: 6,523 
  • Modeled Residue Count: 703 
  • Deposited Residue Count: 714 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43714Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0005780
EC: 3.6.4.13
UniProt
Find proteins for G0RY84 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RY84 
Go to UniProtKB:  G0RY84
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RY84
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MRD

Query on MRD



Download:Ideal Coordinates CCD File
L [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4

Query on SO4



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

Query on BEF



Download:Ideal Coordinates CCD File
C [auth A]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.199 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.826α = 90
b = 105.637β = 90
c = 119.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description