376D

A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)

• PDB DOI: https://doi.org/10.2210/pdb376D/pdb
• NAKB: 376D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-01-22 Released: 1999-10-26 
• Deposition Author(s): Cruse, W.B.T., Shepard, W., Prange, T., delalFortelle, E., Fourme, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.

Shepard, W., Cruse, W.B., Fourme, R., de la Fortelle, E., Prange, T.

(1998) Structure 6: 849-861

• PubMed: 9687367 
• DOI: https://doi.org/10.1016/s0969-2126(98)00087-2
• Primary Citation of Related Structures:  
  376D


• PubMed Abstract: 
  

  The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood.

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Organizational Affiliation: 

LURE, Université Paris-Sud, Orsay, France. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3 kDa 
• Atom Count: 206 
• Modelled Residue Count: 9 
• Deposited Residue Count: 9 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')	A	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	B [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.56	α = 90
b = 37.56	β = 90
c = 65.39	γ = 120

Software Package:

Software Name	Purpose
MADLSQ	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
MADLSQ	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-26 
Deposition Author(s): Cruse, W.B.T., Shepard, W., Prange, T., delalFortelle, E., Fourme, R.

Revision History  

• Version 1.0: 1999-10-26
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description