2GZK

Structure of a complex of tandem HMG boxes and DNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a Complex of Tandem HMG Boxes and DNA.

Stott, K.Tang, G.S.Lee, K.B.Thomas, J.O.

(2006) J Mol Biol 360: 90-104

  • DOI: 10.1016/j.jmb.2006.04.059
  • Primary Citation of Related Structures:  
    2GZK

  • PubMed Abstract: 
  • The high-mobility group protein HMGB1 contains two tandem DNA-binding HMG box domains, A and B, linked by a short flexible linker that allows the two domains to behave independently in the free protein. There is no structural information on how the linked domains and linker behave when bound to DNA, mainly due to the lack of any DNA-sequence preference of HMGB1 ...

    The high-mobility group protein HMGB1 contains two tandem DNA-binding HMG box domains, A and B, linked by a short flexible linker that allows the two domains to behave independently in the free protein. There is no structural information on how the linked domains and linker behave when bound to DNA, mainly due to the lack of any DNA-sequence preference of HMGB1. We report the structure determination, by NMR spectroscopy, of a well-defined complex of two tandem HMG boxes bound to a 16 bp oligonucleotide. The protein is an engineered version of the AB di-domain of HMGB1, in which the A box has been replaced by the HMG box of the sequence-specific transcription factor SRY, to give SRY.B. In the SRY.B/DNA complex, both HMG boxes bind in the minor groove and contribute to the overall DNA bending by intercalation of bulky hydrophobic residues between base-pairs; the bends reinforce each other, and the basic linker lies partly in the minor groove. As well as being the first structure of an HMG-box di-domain bound to DNA, this provides the first structure of the B domain of HMGB1 bound to DNA.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sex-determining region on Y / HMGB1C [auth A]159Homo sapiensRattus rattus
This entity is chimeric
Mutation(s): 0 
Gene Names: SRY
UniProt & NIH Common Fund Data Resources
Find proteins for P63159 (Rattus norvegicus)
Explore P63159 
Go to UniProtKB:  P63159
Find proteins for Q05066 (Homo sapiens)
Explore Q05066 
Go to UniProtKB:  Q05066
PHAROS:  Q05066
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP*C)-3'A [auth B]16N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*C)-3'B [auth C]16N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Binding Affinity Annotations 
      IDSourceBinding Affinity
      DNA PDBBind:  2GZK Kd: 140 (nM) from 1 assay(s)
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Calculated: 100 
      • Conformers Submitted: 
      • Selection Criteria: structures with the lowest energy 
      • OLDERADO: 2GZK Olderado

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2006-07-25
        Type: Initial release
      • Version 1.1: 2008-05-01
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance