8RDY

Saccharomyces cerevisiae Prp43 helicase in complex with Pxr1

• PDB DOI: https://doi.org/10.2210/pdb8RDY/pdb
• EM Map EMD-19078: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae, Schistosoma japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-08 Released: 2024-10-23 
• Deposition Author(s): Rabl, J., Portugal Calisto, D., Panse, V.G.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly

Portugal Hnizda Calisto, D., Rabl, J., Panse, V.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 134.45 kDa 
• Atom Count: 5,504 
• Modelled Residue Count: 680 
• Deposited Residue Count: 1,172 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43	A	804	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRP43 EC: 3.6.4.13
UniProt
Find proteins for P53131 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53131  Go to UniProtKB:  P53131

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase class-mu 26 kDa isozyme,Protein PXR1	B	368	Schistosoma japonicum, Saccharomyces cerevisiae This entity is chimeric	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for P53335 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53335  Go to UniProtKB:  P53335
Find proteins for P08515 (Schistosoma japonicum) Explore P08515  Go to UniProtKB:  P08515
UniProt Groups	P53335P08515

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Rabl, J., Portugal Calisto, D., Panse, V.G.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	NCCR RNA & Disease

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release