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: 1 
  • Selection Criteria: LOWEST RESTRAINT ENERGY 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biol 5: 579-584

  • DOI: 10.1038/836
  • Primary Citation of Related Structures:  
    1BBX

  • 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 affinity ...

    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 Biol 1: 808
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-BINDING PROTEIN 7DC, D63Saccharolobus solfataricusMutation(s): 0 
UniProt
Find proteins for P39476 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P39476 
Go to UniProtKB:  P39476
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39476
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3')A, B 12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 1 
  • Selection Criteria: LOWEST RESTRAINT ENERGY 
  • OLDERADO: 1BBX Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Database references, Derived calculations, Other