1BBX

NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST RESTRAINT ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Architecture of Nonspecific Protein-DNA Interactions in the Sso7D-DNA Complex

Agback, P.Baumann, H.Knapp, S.Ladenstein, R.Hard, T.

(1998) Nat.Struct.Mol.Biol. 5: 579-584

  • DOI: 10.1038/836

  • PubMed Abstract: 
  • Many biochemical processes, including DNA packing, maintenance and control, rely on non-sequence specific protein-DNA interactions. Nonspecific DNA-binding proteins have evolved to tolerate a wide range of DNA sequences, yet bind with a respectable a ...

    Many biochemical processes, including DNA packing, maintenance and control, rely on non-sequence specific protein-DNA interactions. Nonspecific DNA-binding proteins have evolved to tolerate a wide range of DNA sequences, yet bind with a respectable affinity. The nonspecific binding requirement is in contrast to that imposed on, for example, transcription factors and implies a different structural basis for the biomolecular recognition process. To address this issue, and the mechanism for archaeal DNA packing, we determined the structure of the Sso7d protein from Sulfolobus solfataricus in complex with DNA. Sso7d binds DNA by placing a triple-stranded beta-sheet across the DNA minor groove. The protein is anchored in this position by the insertion of hydrogen bond-donating side chains into the groove and additionally stabilized by electrostatic and non-polar interactions with the DNA backbone. This structure explains how strong binding can be achieved independent of DNA sequence. Sso7d binding also distorts the DNA conformation and introduces significant unwinding of the helix. This effect suggests a mechanism for DNA packing in Sulfolobus based on negative DNA supercoiling.


    Related Citations: 
    • DNA-Binding Surface of the Sso7D Protein from Sulfolobus Solfataricus
      Baumann, H.,Knapp, S.,Karshikoff, A.,Ladenstein, R.,Hard, T.
      (1995) J.Mol.Biol. 247: 840
    • Solution Structure and DNA-Binding Properties of a Thermostable Protein from the Archaeon Sulfolobus Solfataricus
      Baumann, H.,Knapp, S.,Lundback, T.,Ladenstein, R.,Hard, T.
      (1994) Nat.Struct.Mol.Biol. 1: 808


    Organizational Affiliation

    Center for Structural Biochemistry, Department of Biotechnology, The Royal Institute of Technology (KTH), Huddinge, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-BINDING PROTEIN 7D
C, D
63Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: sso7d (sso7d-1)
Find proteins for P39476 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P39476
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3')A,B12N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST RESTRAINT ENERGY 
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance