1B4Y | pdb_00001b4y

STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN INTRAMOLECULAR DNA TRIPLE HELIX.

• PDB DOI: https://doi.org/10.2210/pdb1B4Y/pdb
• NAKB: 1B4Y
• BMRB: 4400

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-12-30 Released: 1999-09-13 
• Deposition Author(s): Van Dongen, M.J.P., Doreleijers, J.F., Van Der Marel, G.A., Van Boom, J.H., Hilbers, C.W., Wijmenga, S.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 12 
• Selection Criteria: LOW ENERGIES 

Literature

Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix.

van Dongen, M.J., Doreleijers, J.F., van der Marel, G.A., van Boom, J.H., Hilbers, C.W., Wijmenga, S.S.

(1999) Nat Struct Biol 6: 854-859

• PubMed: 10467098 
• DOI: https://doi.org/10.1038/12313
• Primary Citation Related Structures: 
  1B4Y


• PubMed Abstract: 
  

  H-DNA, thought to play a regulatory role in transcription, exists in two isomeric forms, H-y3 and H-y5. We present the first solution structure of a DNA fragment representing the H-y5 fold. The structure shows the H-y5 triple helix, and for the first time how in an H-DNA isomer the purine strand extension interacts with the triplex loop. It gives direct insight into the mechanism of H-DNA formation, and explains a host of biochemical and biophysical data on the relative stability of the H-DNA isomers. In addition, the observed interaction of the purine strand extension and the triplex loop provides new clues to the design of clamp-type triple helix-forming oligonucleotides.

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Organizational Affiliation: 
• NSR Centre for Molecular Structure, Design, and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.07 kDa 
• Atom Count: 599 
• Modeled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (H-Y5 TRIPLE HELIX)	A	30	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 12 
• Selection Criteria: LOW ENERGIES 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-09-13 
Deposition Author(s): Van Dongen, M.J.P., Doreleijers, J.F., Van Der Marel, G.A., Van Boom, J.H., Hilbers, C.W., Wijmenga, S.S.

Revision History  

• Version 1.0: 1999-09-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-23
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection