3IBK | pdb_00003ibk

Crystal structure of a telomeric RNA quadruplex

• PDB DOI: https://doi.org/10.2210/pdb3IBK/pdb
• NAKB: 3IBK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-07-16 Released: 2010-05-12 
• Deposition Author(s): Collie, G.W., Neidle, S., Parkinson, G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.231 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex

Collie, G.W., Haider, S.M., Neidle, S., Parkinson, G.N.

(2010) Nucleic Acids Res 38: 5569-5580

• PubMed: 20413582 
• DOI: https://doi.org/10.1093/nar/gkq259
• Primary Citation Related Structures: 
  3IBK


• PubMed Abstract: 
  

  DNA telomeric repeats in mammalian cells are transcribed to guanine-rich RNA sequences, which adopt parallel-stranded G-quadruplexes with a propeller-like fold. The successful crystallization and structure analysis of a bimolecular human telomeric RNA G-quadruplex, folded into the same crystalline environment as an equivalent DNA oligonucleotide sequence, is reported here. The structural basis of the increased stability of RNA telomeric quadruplexes over DNA ones and their preference for parallel topologies is described here. Our findings suggest that the 2'-OH hydroxyl groups in the RNA quadruplex play a significant role in redefining hydration structure in the grooves and the hydrogen bonding networks. The preference for specific nucleotides to populate the C3'-endo sugar pucker domain is accommodated by alterations in the phosphate backbone, which leads to greater stability through enhanced hydrogen bonding networks. Molecular dynamics simulations on the DNA and RNA quadruplexes are consistent with these findings. The computations, based on the native crystal structure, provide an explanation for RNA G-quadruplex ligand binding selectivity for a group of naphthalene diimide ligands as compared to the DNA G-quadruplex.

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Organizational Affiliation: 
• Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, UK.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 8.05 kDa 
• Atom Count: 567 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(5BU)P*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.231 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.583	α = 90
b = 57.583	β = 90
c = 38.377	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Collie, G.W., Neidle, S., Parkinson, G.N.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2014-02-19
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description