2AQY

(3+1) assembly of three human telomeric DNA repeats into an asymmetrical dimeric G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb2AQY/pdb
• NAKB: 2AQY

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-08-18 Released: 2006-03-07 
• Deposition Author(s): Zhang, N., Phan, A.T., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function 

Literature

(3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex

Zhang, N., Phan, A.T., Patel, D.J.

(2005) J Am Chem Soc 127: 17277-17285

• PubMed: 16332077 
• DOI: https://doi.org/10.1021/ja0543090
• Primary Citation of Related Structures:  
  2AQY


• PubMed Abstract: 
  

  We present an NMR study on the structure of a DNA fragment of the human telomere containing three guanine-tracts, d(GGGTTAGGGTTAGGGT). This sequence forms in Na(+) solution a unique asymmetric dimeric quadruplex, in which the G-tetrad core involves all three G-tracts of one strand and only the last 3'-end G-tract of the other strand. We show that a three-repeat human telomeric sequence can also associate with a single-repeat human telomeric sequence into a structure with the same topology that we name (3 + 1) quadruplex assembly. In this G-quadruplex assembly, there are one syn.syn.syn.anti and two anti.anti.anti.syn G-tetrads, two edgewise loops, three G-tracts oriented in one direction and the fourth oriented in the opposite direction. We discuss the possible implications of the new folding topology for understanding the structure of telomeric DNA, including t-loop formation, and for targeting G-quadruplexes in the telomeres.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.9 kDa 
• Atom Count: 459 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*(OIP)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'	A	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*GP*GP*GP*(DU))-3'	B	6	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Zhang, N., Phan, A.T., Patel, D.J.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations