3KX2

Crystal structure of Prp43p in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb3KX2/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-02 Released: 2010-01-26 
• Deposition Author(s): Nielsen, K.H., Andersen, G.R., He, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Structural basis for the function of DEAH helicases

He, Y., Andersen, G.R., Nielsen, K.H.

(2010) EMBO Rep 11: 180-186

• PubMed: 20168331 
• DOI: https://doi.org/10.1038/embor.2010.11
• Primary Citation of Related Structures:  
  3KX2


• PubMed Abstract: 
  

  DEAH helicases participate in pre-messenger RNA splicing and ribosome biogenesis. The structure of yeast Prp43p-ADP reveals the homology of DEAH helicases to DNA helicases and the presence of an oligonucleotide-binding motif. A beta-hairpin from the second RecA domain is wedged between two carboxy-terminal domains and blocks access to the occluded RNA binding site formed by the RecA domains and a C-terminal domain. ATP binding and hydrolysis are likely to induce conformational changes in the hairpin that are important for RNA unwinding or ribonucleoprotein remodelling. The structure of Prp43p provides the framework for functional and genetic analysis of all DEAH helicases.

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Organizational Affiliation: 

Department of Molecular Biology, Aarhus University, Aarhus, Denmark.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.27 kDa 
• Atom Count: 13,172 
• Modelled Residue Count: 1,510 
• Deposited Residue Count: 1,534 
• 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 [auth B], B [auth A]	767	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YGL120C EC: 3.6.1
UniProt
Find proteins for P53131 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53131  Go to UniProtKB:  P53131

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth B], F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth B], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.250 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.152	α = 90
b = 118.152	β = 90
c = 253.601	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Nielsen, K.H., Andersen, G.R., He, Y.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Data collection, Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations