2OEH

Determination of the Three-dimensional Structure of the Mrf2-DNA Complex Using Paramagnetic Spin Labeling


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling.

Cai, S.Zhu, L.Zhang, Z.Chen, Y.

(2007) Biochemistry 46: 4943-4950

  • DOI: 10.1021/bi061738h

  • PubMed Abstract: 
  • Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. At present, NMR spectroscopy is the only approach that can provide atomic details of prot ...

    Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. At present, NMR spectroscopy is the only approach that can provide atomic details of protein-DNA recognition in solution. However, determining the structures of protein-DNA complexes using NMR spectroscopy has been dependent on the observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which are difficult to obtain in many cases. In this study, we have shown that intermolecular distance constraints derived from a single spin-label in combination with docking calculations have defined many specific contacts of the complex between the AT-rich interaction domain (ARID) of Mrf2 and its target DNA. Mrf2 contacts DNA mainly using the two flexible loops, L1 and L2. While the L1 loop contacts the phosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in the major groove of DNA. Despite the structural diversity in the ARID family of DNA-binding proteins, Mrf2 maintains contacts with DNA similar to those observed in the homologous Dri-DNA complex.


    Organizational Affiliation

    Division of Immunology, Beckman Research Institute of the City of Hope, 1500 Duarte Road, Duarte, California 91006, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AT-rich interactive domain-containing protein 5B
A
107Homo sapiensMutation(s): 0 
Gene Names: ARID5B (DESRT, MRF2)
Find proteins for Q14865 (Homo sapiens)
Go to Gene View: ARID5B
Go to UniProtKB:  Q14865
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*TP*AP*CP*AP*AP*TP*AP*TP*AP*AP*CP*GP*TP*CP*G)-3'B15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*GP*AP*CP*GP*TP*TP*AP*TP*AP*TP*TP*GP*T)-3'C14N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2OEH Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance