1GQU

Crystal structure of an alternating A-T oligonucleotide fragment with Hoogsteen base pairing

• PDB DOI: https://doi.org/10.2210/pdb1GQU/pdb
• NAKB: 1GQU

• Classification: DNA
• Mutation(s): No 


• Deposited: 2001-12-05 Released: 2002-12-05 
• Deposition Author(s): Abrescia, N.G.A., Thompson, A., Huynh-Dinh, T., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

Crystal Structure of an Antiparallel DNA Fragment with Hoogsteen Base Pairing

Abrescia, N.G.A., Thompson, A., Huynh-Dinh, T., Subirana, J.A.

(2002) Proc Natl Acad Sci U S A 99: 2806

• PubMed: 11880632 
• DOI: https://doi.org/10.1073/pnas.052675499
• Primary Citation of Related Structures:  
  1GQU


• PubMed Abstract: 
  

  We report here an alternative double-helical structure of the DNA molecule. It has been found in the d(ATA(Br)UAT) and d(ATATAT) sequences by single-crystal x-ray crystallography. This sequence is found not only in TATA boxes, but also in other regulatory regions of DNA. Bases of the two antiparallel strands form Hoogsteen pairs, with adenines in the syn conformation. The structure is related neither to those found in triple helices nor to parallel DNA duplexes. Its conformational parameters are very similar to those of duplex DNA in the B form. Both forms may coexist under physiological conditions, although the Hoogsteen pairing greatly influences the recognition sites on DNA. Our results demonstrate that an alternative to the classical B-DNA double helix is possible.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological Assembly 2  

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

Macromolecule Content

• Total Structure Weight: 7.49 kDa 
• Atom Count: 527 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.96	α = 90
b = 48.95	β = 93.27
c = 32.24	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SCALEIT	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-05 
Deposition Author(s): Abrescia, N.G.A., Thompson, A., Huynh-Dinh, T., Subirana, J.A.

Revision History  

• Version 1.0: 2002-12-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other