1CA5

INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs

Su, S.Gao, Y.-G.Robinson, H.Liaw, Y.C.Edmondson, S.P.Shriver, J.W.Wang, A.H.-J.

(2000) J Mol Biol 303: 395-403

  • DOI: 10.1006/jmbi.2000.4112
  • Primary Citation of Related Structures:  
    1C8C, 1CA5, 1CA6

  • PubMed Abstract: 
  • Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1 ...

    Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation.


    Related Citations: 
    • The hyperthermophile chromosomal protein Sac7d sharply kinks DNA.
      Robinson, H., Gao, Y.G., McCrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.
      (1998) Nature 392: 202
    • The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
      Gao, Y.G., Su, S.Y., Robinson, H., Padmanabhan, S., Lim, L., McCrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.
      (1998) Nat Struct Biol 5: 782

    Organizational Affiliation

    Center for Biophysics and COmputational BIology, University of Illinois at Urbana-Champaign, 61801, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CHROMOSOMAL PROTEIN SAC7DC [auth A]66Sulfolobus acidocaldariusMutation(s): 0 
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore P13123 
Go to UniProtKB:  P13123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13123
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3'A [auth B],
B [auth C]
8synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.78α = 90
b = 76.76β = 90
c = 35.14γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-23
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-28
    Changes: Advisory
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2019-11-06
    Changes: Data collection, Database references, Source and taxonomy