Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Macromolecule Content

• Total Structure Weight: 4.66 kDa 
• Atom Count: 331 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

4XK0

Crystal structure of a tetramolecular RNA G-quadruplex in potassium

• PDB DOI: 10.2210/pdb4XK0/pdb
• NDB: 4XK0

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-01-09 Released: 2015-02-11 
• Deposition Author(s): Chen, M.C., Murat, P., Abecassis, K.A., Ferre-D'Amare, A.R., Balasubramanian, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.144 
• R-Value Work: 0.144 

Literature

Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase.

Chen, M.C., Murat, P., Abecassis, K., Ferre-D'Amare, A.R., Balasubramanian, S.

(2015) Nucleic Acids Res 43: 2223-2231

• PubMed: 25653156 
• DOI: 10.1093/nar/gkv051
• Primary Citation of Related Structures:  
  4XK0


• PubMed Abstract: 
  

The unwinding of nucleic acid secondary structures within cells is crucial to maintain genomic integrity and prevent abortive transcription and translation initiation. DHX36, also known as RHAU or G4R1, is a DEAH-box ATP-dependent helicase highly specific for DNA and RNA G-quadruplexes (G4s). A fundamental mechanistic understanding of the interaction between helicases and their G4 substrates is important to elucidate G4 biology and pave the way toward G4-targeted therapies. Here we analyze how the thermodynamic stability of G4 substrates affects binding and unwinding by DHX36. We modulated the stability of the G4 substrates by varying the sequence and the number of G-tetrads and by using small, G4-stabilizing molecules. We found an inverse correlation between the thermodynamic stability of the G4 substrates and rates of unwinding by DHX36. In stark contrast, the ATPase activity of the helicase was largely independent of substrate stability pointing toward a decoupling mechanism akin to what has been observed for many double-stranded DEAD-box RNA helicases. Our study provides the first evidence that DHX36 uses a local, non-processive mechanism to unwind G4 substrates, reminiscent of that of eukaryotic initiation factor 4A (eIF4A) on double-stranded substrates.

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Organizational Affiliation: 

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-(*UP*GP*GP*GP*GP*U)-3')	A, B [auth C]	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	H [auth A], I [auth A], N [auth C]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
K	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth C], K [auth C], L [auth C], M [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.144 
• R-Value Work: 0.144 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.133	α = 90
b = 33.133	β = 90
c = 54.843	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-09 
• Released Date: 2015-02-11 
Deposition Author(s): Chen, M.C., Murat, P., Abecassis, K.A., Ferre-D'Amare, A.R., Balasubramanian, S.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 1.2: 2015-03-11
  Changes: Database references
• Version 1.3: 2015-08-19
  Changes: Refinement description