2LOD | pdb_00002lod

Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops

• PDB DOI: https://doi.org/10.2210/pdb2LOD/pdb
• NAKB: 2LOD
• BMRB: 18209

• Classification: DNA
• Mutation(s): No 


• Deposited: 2012-01-23 Released: 2012-05-30 
• Deposition Author(s): Marusic, M., Sket, P., Bauer, L., Viglasky, V., Plavec, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops.

Marusic, M., Sket, P., Bauer, L., Viglasky, V., Plavec, J.

(2012) Nucleic Acids Res 40: 6946-6956

• PubMed: 22532609 
• DOI: https://doi.org/10.1093/nar/gks329
• Primary Citation Related Structures: 
  2LOD


• PubMed Abstract: 
  

  We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G(3)ATG(3)ACACAG(4)ACG(3)] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present.

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Organizational Affiliation: 
• Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Slovenia.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.97 kDa 
• Atom Count: 465 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*CP*GP*GP*G)-3')	A	22	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Marusic, M., Sket, P., Bauer, L., Viglasky, V., Plavec, J.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references