2A5R

Complex of tetra-(4-n-methylpyridyl) porphin with monomeric parallel-stranded DNA tetraplex, snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, C-MYC promoter, NMR, 6 struct.

• PDB DOI: https://doi.org/10.2210/pdb2A5R/pdb
• NAKB: 2A5R

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-06-30 Released: 2005-07-26 
• Deposition Author(s): Phan, A.T., Kuryavyi, V.V., Gaw, H.Y., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 6 
• Conformers Submitted: 6 
• Selection Criteria: structures with the least restraint violations 

Literature

Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.

Phan, A.T., Kuryavyi, V., Gaw, H.Y., Patel, D.J.

(2005) Nat Chem Biol 1: 167-173

• PubMed: 16408022 
• DOI: https://doi.org/10.1038/nchembio723
• Primary Citation of Related Structures:  
  2A5P, 2A5R


• PubMed Abstract: 
  

  It has been widely accepted that DNA can adopt other biologically relevant structures beside the Watson-Crick double helix. One recent important example is the guanine-quadruplex (G-quadruplex) structure formed by guanine tracts found in the MYC (or c-myc) promoter region, which regulates the transcription of the MYC oncogene. Stabilization of this G-quadruplex by ligands, such as the cationic porphyrin TMPyP4, decreases the transcriptional level of MYC. Here, we report the first structure of a DNA fragment containing five guanine tracts from this region. An unusual G-quadruplex fold, which was derived from NMR restraints using unambiguous model-independent resonance assignment approaches, involves a core of three stacked guanine tetrads formed by four parallel guanine tracts with all anti guanines and a snapback 3'-end syn guanine. We have determined the structure of the complex formed between this G-quadruplex and TMPyP4. This structural information, combined with details of small-molecule interaction, provides a platform for the design of anticancer drugs targeting multi-guanine-tract sequences that are found in the MYC and other oncogenic promoters, as well as in telomeres.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.38 kDa 
• Atom Count: 566 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'	A	24	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POH	B [auth A]	(1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin C44 H38 N8 ABCGFHPGHXSVKI-LWQDQPMZSA-O

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 6 
• Conformers Submitted: 6 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Phan, A.T., Kuryavyi, V.V., Gaw, H.Y., Patel, D.J.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance