241D

EXTENSION OF THE FOUR-STRANDED INTERCALATED CYTOSINE MOTIF BY ADENINE.ADENINE BASE PAIRING IN THE CRYSTAL STRUCTURE OF D(CCCAAT)

• PDB DOI: https://doi.org/10.2210/pdb241D/pdb
• NAKB: 241D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1995-12-07 Released: 1996-04-03 
• Deposition Author(s): Berger, I., Kang, C., Fredian, A., Ratliff, R., Moyzis, R., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Literature

Extension of the four-stranded intercalated cytosine motif by adenine.adenine base pairing in the crystal structure of d(CCCAAT).

Berger, I., Kang, C., Fredian, A., Ratliff, R., Moyzis, R., Rich, A.

(1995) Nat Struct Biol 2: 416-425

• PubMed: 7664099 
• DOI: https://doi.org/10.1038/nsb0595-416
• Primary Citation of Related Structures:  
  241D


• PubMed Abstract: 
  

  The crystal structure of d(CCCAAT), refined at 2.0 A resolution, shows a four stranded molecule in which two parallel duplexes intercalate with opposite polarity, using cytosine.protonated cytosine base pairs. The intercalation motif in this structure is extended by adenine.adenine base pairs. Two topologically distinct broad grooves are found in the lath-like central part of the molecule with the phosphate groups on one side bent over towards each other, stabilized by bridging water molecules. At the 3' ends, two arrangements of intermolecular A.A.T base triplets are found, involving both asymmetric and symmetric A.A base pairs joined to thymine residues by Watson-Crick and reverse Hoogsteen base pairing, respectively.

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.51 kDa 
• Atom Count: 289 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.18	α = 90
b = 32.18	β = 90
c = 52.49	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-03 
Deposition Author(s): Berger, I., Kang, C., Fredian, A., Ratliff, R., Moyzis, R., Rich, A.

Revision History  

• Version 1.0: 1996-04-03
  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: 2024-02-14
  Changes: Data collection, Database references