5DTU | pdb_00005dtu

Crystal structure of the RNA-helicase Prp28 from Chaetomium thermophilum bound to ADP

• PDB DOI: https://doi.org/10.2210/pdb5DTU/pdb

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


• Deposited: 2015-09-18 Released: 2016-05-04 
• 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: 3.20 Å
• R-Value Free: 
  0.288 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.279 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of the spliceosomal RNA helicase Prp28 from the thermophilic eukaryote Chaetomium thermophilum.

Tauchert, M.J., Ficner, R.

(2016) Acta Crystallogr F Struct Biol Commun 72: 409-416

• PubMed: 27139834 
• DOI: https://doi.org/10.1107/S2053230X16006038
• Primary Citation Related Structures: 
  5DTU


• PubMed Abstract: 
  

  Prp28 (pre-mRNA-splicing ATP-dependent RNA helicase 28) is a spliceosomal DEAD-box helicase which is involved in two steps of spliceosome assembly. It is required for the formation of commitment complex 2 in an ATP-independent manner as well as for the formation of the pre-catalytic spliceosome, which in contrast is ATP-dependent. During the latter step, Prp28 is crucial for the integration of the U4/U6·U5 tri-snRNP since it displaces the U1 snRNP and allows the U6 snRNP to base-pair with the 5'-splice site. Here, the crystal structure of Prp28 from the thermophilic fungus Chaetomium thermophilum is reported at 3.2 Å resolution and is compared with the available structures of homologues.

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Organizational Affiliation: 
• Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University 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: 53.42 kDa 
• Atom Count: 3,166 
• Modeled Residue Count: 404 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prp28	A	475	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0054430 EC: 3.6.4.13
UniProt
Find proteins for G0SBQ7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SBQ7  Go to UniProtKB:  G0SBQ7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.288 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.279 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.5	α = 90
b = 50.4	β = 101.4
c = 65.8	γ = 90

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: 2016-05-04 
Deposition Author(s): Tauchert, M.J., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB860

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-05-11
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Refinement description