5ORQ | pdb_00005orq

Crystal structure of designed cPPR-Telo1 in complex with ssDNA

• PDB DOI: https://doi.org/10.2210/pdb5ORQ/pdb
• NAKB: 5ORQ

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


• Deposited: 2017-08-16 Released: 2018-06-20 
• Deposition Author(s): Spahr, H., Rackham, O.
• Funding Organization(s): Australian Research Council, National Health and Medical Research Council, Cancer Council Western Australia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.228 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.

Spahr, H., Chia, T., Lingford, J.P., Siira, S.J., Cohen, S.B., Filipovska, A., Rackham, O.

(2018) Nat Commun 9: 2212-2212

• PubMed: 29880855 
• DOI: https://doi.org/10.1038/s41467-018-04388-1
• Primary Citation Related Structures: 
  5ORM, 5ORQ


• PubMed Abstract: 
  

  DNA is typically found as a double helix, however it must be separated into single strands during all phases of DNA metabolism; including transcription, replication, recombination and repair. Although recent breakthroughs have enabled the design of modular RNA- and double-stranded DNA-binding proteins, there are currently no tools available to manipulate single-stranded DNA (ssDNA). Here we show that artificial pentatricopeptide repeat (PPR) proteins can be programmed for sequence-specific ssDNA binding. Interactions occur using the same code and specificity as for RNA binding. We solve the structures of DNA-bound and apo proteins revealing the basis for ssDNA binding and how hydrogen bond rearrangements enable the PPR structure to envelope its ssDNA target. Finally, we show that engineered PPRs can be designed to bind telomeric ssDNA and can block telomerase activity. The modular mode of ssDNA binding by PPR proteins provides tools to target ssDNA and to understand its importance in cells.

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Organizational Affiliation: 
• Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931, Cologne, Germany.
Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia.
Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia.
School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia. [e-mail].
School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 43.32 kDa 
• Atom Count: 3,372 
• Modeled Residue Count: 374 
• Deposited Residue Count: 374 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cPPR-Telo1	A	364	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')	B	10	Homo sapiens

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.228 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.831	α = 90
b = 114.831	β = 90
c = 83.545	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Spahr, H., Rackham, O.

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Funding Organization	Location	Grant Number
Australian Research Council	Australia	FT0991008, FT0991113, DP140104111
National Health and Medical Research Council	Australia	APP1058442, APP1045677
Cancer Council Western Australia	Australia	--

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary