2EZD

SOLUTION STRUCTURE OF A COMPLEX OF THE SECOND DNA BINDING DOMAIN OF HUMAN HMG-I(Y) BOUND TO DNA DODECAMER CONTAINING THE PRDII SITE OF THE INTERFERON-BETA PROMOTER, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 35 
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.

Huth, J.R.Bewley, C.A.Nissen, M.S.Evans, J.N.Reeves, R.Gronenborn, A.M.Clore, G.M.

(1997) Nat.Struct.Mol.Biol. 4: 657-665

  • Primary Citation of Related Structures:  2EZF, 2EZE, 2EZG

  • PubMed Abstract: 
  • The solution structure of a complex between a truncated form of HMG-I(Y), consisting of the second and third DNA binding domains (residues 51-90), and a DNA dodecamer containing the PRDII site of the interferon-beta promoter has been solved by multid ...

    The solution structure of a complex between a truncated form of HMG-I(Y), consisting of the second and third DNA binding domains (residues 51-90), and a DNA dodecamer containing the PRDII site of the interferon-beta promoter has been solved by multidimensional nuclear magnetic resonance spectroscopy. The stoichiometry of the complex is one molecule of HMG-I(Y) to two molecules of DNA. The structure reveals a new architectural minor groove binding motif which stabilizes B-DNA, thereby facilitating the binding of other transcription factors in the opposing major groove. The interactions involve a central Arg-Gly-Arg motif together with two other modules that participate in extensive hydrophobic and polar contracts. The absence of one of these modules in the third DNA binding domain accounts for its-100 fold reduced affinity relative to the second one.


    Organizational Affiliation

    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-Y
A
25Homo sapiensGene Names: HMGA1 (HMGIY)
Find proteins for P17096 (Homo sapiens)
Go to Gene View: HMGA1
Go to UniProtKB:  P17096
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3')B12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3')C12N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 35 
  • Conformers Submitted: 
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance