103D | pdb_0000103d

THE UNUSUAL STRUCTURE OF THE HUMAN CENTROMERE (GGA)2 MOTIF: UNPAIRED GUANOSINE RESIDUES STACKED BETWEEN SHEARED G(DOT)A PAIRS

• PDB DOI: https://doi.org/10.2210/pdb103D/pdb
• NAKB: 103D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-12-16 Released: 1995-03-31 
• Deposition Author(s): Chou, S.-H., Zhu, L., Reid, B.R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs.

Chou, S.H., Zhu, L., Reid, B.R.

(1994) J Mol Biology 244: 259-268

• PubMed: 7966337 
• DOI: https://doi.org/10.1006/jmbi.1994.1727
• Primary Citation Related Structures: 
  103D


• PubMed Abstract: 
  

  The centromere of human chromosomes contains multiple repeats of the DNA sequence d(TGGAA)n. This sequence has the interesting property of pairing with itself to form stable duplexes. We have determined the solution structure of the unusual DNA duplex 5'-TGGAATGGAA:TGGAATGGAA-3' at atomic resolution. The duplex contains unpaired staggered guanosine residues, which co-stack by intercalation between sheared G.A and A.G base-pairs to form an interesting new structural motif, the GA-bracketed G-stack. The TGGAA repeat unit contains six "steps", four of which are not Watson-Crick base-pairs.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, University of Washington, Seattle 98195.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.5 kDa 
• Atom Count: 500 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')	A, B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-03-31 
Deposition Author(s): Chou, S.-H., Zhu, L., Reid, B.R.

Revision History  

• Version 1.0: 1995-03-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection