5D0U

Crystal structure of the RNA-helicase Prp43 from Chaetomium thermophilum bound to ADP

• PDB DOI: https://doi.org/10.2210/pdb5D0U/pdb

• Classification: HYDROLASE
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-03 Released: 2016-02-10 
• Deposition Author(s): Tauchert, M.J., Ficner, R.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Literature

Structural and functional analysis of the RNA helicase Prp43 from the thermophilic eukaryote Chaetomium thermophilum.

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

(2016) Acta Crystallogr F Struct Biol Commun 72: 112-120

• PubMed: 26841761 
• DOI: https://doi.org/10.1107/S2053230X15024498
• Primary Citation of Related Structures:  
  5D0U


• PubMed Abstract: 
  

  RNA helicases are indispensable for all organisms in each domain of life and have implications in numerous cellular processes. The DEAH-box RNA helicase Prp43 is involved in pre-mRNA splicing as well as rRNA maturation. Here, the crystal structure of Chaetomium thermophilum Prp43 at 2.9 Å resolution is revealed. Furthermore, it is demonstrated that Prp43 from C. thermophilum is capable of functionally replacing its orthologue from Saccharomyces cerevisiae in spliceosomal disassembly assays.

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Organizational Affiliation: 

Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.8 kDa 
• Atom Count: 5,729 
• Modelled Residue Count: 705 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43	A	714	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0005780
UniProt
Find proteins for G0RY84 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0RY84  Go to UniProtKB:  G0RY84

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
DMS	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.211	α = 90
b = 152.211	β = 90
c = 92.766	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Tauchert, M.J., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB 860

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description