4U9M

Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds

• PDB DOI: https://doi.org/10.2210/pdb4U9M/pdb
• NAKB: 4U9M

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2014-08-06 Released: 2015-04-01 
• Deposition Author(s): Acosta-Reyes, F.J., Alechaga, E., Subirana, J.A., Campos, J.L.
• Funding Organization(s): Feder funds and the Ministerio de Ciencia e Inovacion, Generalitat de Catalunya, CONACYT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 0.200 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 

Starting Models: experimental

Literature

Structure of the DNA Duplex d(ATTAAT)2 with Hoogsteen Hydrogen Bonds.

Acosta-Reyes, F.J., Alechaga, E., Subirana, J.A., Campos, J.L.

(2015) PLoS One 10: e0120241-e0120241

• PubMed: 25781995 
• DOI: https://doi.org/10.1371/journal.pone.0120241
• Primary Citation of Related Structures:  
  4U9M


• PubMed Abstract: 
  

  The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT)2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.

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Organizational Affiliation: 

Universitat Politècnica de Catalunya, Departament d'Enginyeria Química, Diagonal 647, E-08028, Barcelona, Spain.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.04 kDa 
• Atom Count: 600 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')	A, B, C, D, E	6	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 0.200 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.756	α = 90
b = 42.898	β = 90.04
c = 99.422	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Acosta-Reyes, F.J., Alechaga, E., Subirana, J.A., Campos, J.L.

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Funding Organization	Location	Grant Number
Feder funds and the Ministerio de Ciencia e Inovacion	Spain	BFU-2009-10380
Generalitat de Catalunya	Spain	SRG2009-1208
CONACYT	Mexico	Reg. 212993

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description