2RRQ

DNA oligomer containing propylene cross-linked cyclic 2'-deoxyuridylate dimer

• PDB DOI: https://doi.org/10.2210/pdb2RRQ/pdb
• NAKB: 2RRQ
• BMRB: 11437

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-03-24 Released: 2011-06-08 
• Deposition Author(s): Furuita, K., Murata, S., Jee, J.G., Ichikawa, S., Matsuda, A., Kojima, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Feature of Bent DNA Recognized by HMGB1

Furuita, K., Murata, S., Jee, J.G., Ichikawa, S., Matsuda, A., Kojima, C.

(2011) J Am Chem Soc 133: 5788-5790

• PubMed: 21443191 
• DOI: https://doi.org/10.1021/ja2013399
• Primary Citation of Related Structures:  
  2RRQ, 2RRR


• PubMed Abstract: 
  

  High Mobility Group Box 1 (HMGB1) protein, a potential therapeutic target, binds bent DNAs structure-specifically. Here we report on a crucial structural feature of the bent DNA required for strong binding to HMGB1. NMR structures of two bent DNA oligomers, only one of which binds strongly to HMGB1, revealed that the presence of a pocket structure on the minor groove is crucial for strong binding through penetration of a phenylalanine residue.

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Organizational Affiliation: 

Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.57 kDa 
• Atom Count: 569 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*TP*CP*AP*(JDT)P*TP*AP*CP*AP*TP*CP*C)-3')	A	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*TP*GP*TP*AP*AP*TP*GP*AP*AP*GP*G)-3')	B	14	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Furuita, K., Murata, S., Jee, J.G., Ichikawa, S., Matsuda, A., Kojima, C.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other