4WN4 | pdb_00004wn4

Crystal structure of designed cPPR-polyA protein

• PDB DOI: https://doi.org/10.2210/pdb4WN4/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-10 Released: 2014-12-24 
• Deposition Author(s): Coquille, S.C., Filipovska, A., Chia, T.S., Rajappa, L., Lingford, J.P., Razif, M.F.M., Thore, S., Rackham, O.
• Funding Organization(s): Swiss National Science Foundation, Novartis Foundation for medical-biological research, Australian Research Council, National Health and Medical Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

An artificial PPR scaffold for programmable RNA recognition.

Coquille, S., Filipovska, A., Chia, T., Rajappa, L., Lingford, J.P., Razif, M.F., Thore, S., Rackham, O.

(2014) Nat Commun 5: 5729-5729

• PubMed: 25517350 
• DOI: https://doi.org/10.1038/ncomms6729
• Primary Citation Related Structures: 
  4PJQ, 4PJR, 4PJS, 4WN4, 4WSL


• PubMed Abstract: 
  

  Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.

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Organizational Affiliation: 
• Department of Molecular Biology, University of Geneva, Science III, 30, Quai Ernest-Ansermet, Geneva 4 1211, Switzerland.
1] Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia [2] School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 66.45 kDa 
• Atom Count: 3,216 
• Modeled Residue Count: 420 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentatricopeptide repeat protein	A, B	303	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.85 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.72	α = 90
b = 204.72	β = 90
c = 204.72	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Coquille, S.C., Filipovska, A., Chia, T.S., Rajappa, L., Lingford, J.P., Razif, M.F.M., Thore, S., Rackham, O.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	316030-128787
Swiss National Science Foundation	Switzerland	31003A_140924
Swiss National Science Foundation	Switzerland	31003A_124909
Novartis Foundation for medical-biological research	Switzerland	09A07
Australian Research Council	Australia	FT0991008
Australian Research Council	Australia	FT0991113
Australian Research Council	Australia	DP140104111
National Health and Medical Research Council	Australia	APP1058442
National Health and Medical Research Council	Australia	APP1045677

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary