1QRV

CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition.

Murphy IV, F.V.Sweet, R.M.Churchill, M.E.

(1999) EMBO J 18: 6610-6618

  • DOI: 10.1093/emboj/18.23.6610
  • Primary Citation of Related Structures:  
    1QRV

  • PubMed Abstract: 
  • The high mobility group (HMG) chromosomal proteins, which are common to all eukaryotes, bind DNA in a non-sequence-specific fashion to promote chromatin function and gene regulation. They interact directly with nucleosomes and are believed to be modu ...

    The high mobility group (HMG) chromosomal proteins, which are common to all eukaryotes, bind DNA in a non-sequence-specific fashion to promote chromatin function and gene regulation. They interact directly with nucleosomes and are believed to be modulators of chromatin structure. They are also important in V(D)J recombination and in activating a number of regulators of gene expression, including p53, Hox transcription factors and steroid hormone receptors, by increasing their affinity for DNA. The X-ray crystal structure, at 2.2 A resolution, of the HMG domain of the Drosophila melanogaster protein, HMG-D, bound to DNA provides the first detailed view of a chromosomal HMG domain interacting with linear DNA and reveals the molecular basis of non-sequence-specific DNA recognition. Ser10 forms water-mediated hydrogen bonds to DNA bases, and Val32 with Thr33 partially intercalates the DNA. These two 'sequence-neutral' mechanisms of DNA binding substitute for base-specific hydrogen bonds made by equivalent residues of the sequence-specific HMG domain protein, lymphoid enhancer factor-1. The use of multiple intercalations and water-mediated DNA contacts may prove to be generally important mechanisms by which chromosomal proteins bind to DNA in the minor groove.


    Organizational Affiliation

    Department of Pharmacology, The University of Colorado Health Sciences Center, 4200 E. Ninth Avenue, Denver, CO 80262, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIGH MOBILITY GROUP PROTEIN DAB73Drosophila melanogasterMutation(s): 0 
Gene Names: HmgDCG17950
Find proteins for Q05783 (Drosophila melanogaster)
Explore Q05783 
Go to UniProtKB:  Q05783
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3')C, D10N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NA
    Query on NA

    Download CCD File 
    C
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.238 
    • R-Value Observed: 0.238 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 43.74α = 90
    b = 53.797β = 90
    c = 86.843γ = 90
    Software Package:
    Software NamePurpose
    SOLVEphasing
    SHARPphasing
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1999-12-18
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-01-31
      Changes: Database references