1H5P

Solution structure of the human Sp100b SAND domain by heteronuclear NMR.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: ACCEPTABLE COVALENT GEOMETRY, FAVOURABLE NON-BOND ENERGY, FEWEST RESTRAINT VIOLATIONS, LOWEST OVERALL ENERGIES 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.

Bottomley, M.J., Collard, M.W., Huggenvik, J.I., Liu, Z., Gibson, T.J., Sattler, M.

(2001) Nat Struct Biol 8: 626-633

  • DOI: 10.1038/89675
  • Primary Citation of Related Structures:  
    1H5P

  • PubMed Abstract: 

    • The SAND domain is a conserved sequence motif found in a number of nuclear proteins, including the Sp100 family and NUDR. These are thought to play important roles in chromatin-dependent transcriptional regulation and are linked to many diseases. We have determined the three-dimensional (3D) structure of the SAND domain from Sp100b ...

    The SAND domain is a conserved sequence motif found in a number of nuclear proteins, including the Sp100 family and NUDR. These are thought to play important roles in chromatin-dependent transcriptional regulation and are linked to many diseases. We have determined the three-dimensional (3D) structure of the SAND domain from Sp100b. The structure represents a novel alpha/beta fold, in which a conserved KDWK sequence motif is found within an alpha-helical, positively charged surface patch. For NUDR, the SAND domain is shown to be sufficient to mediate DNA binding. Using mutational analyses and chemical shift perturbation experiments, the DNA binding surface is mapped to the alpha-helical region encompassing the KDWK motif. The DNA binding activity of wild type and mutant proteins in vitro correlates with transcriptional regulation activity of full length NUDR in vivo. The evolutionarily conserved SAND domain defines a new DNA binding fold that is involved in chromatin-associated transcriptional regulation.

    Related Citations: 
    • Nuclear Deaf-1-Related (Nudr) Protein Contains a Novel DNA Binding Domain and Represses Transcription of the Heterogeneous Nuclear Ribonucleoprotein A2/B1 Promoter
      Michelson, R.J., Collard, M.W., Ziemba, A.J., Persinger, J., Bartholomew, B., Huggenvik, J.I.
      (1999) J Biol Chem 274: 30510
    • The Apeced Polyglandular Autoimmune Syndrome Protein, Aire-1, Contains the Sand Domain and is Probably a Transcription Factor
      Gibson, T.J., Ramu, C., Gemuend, C., Aasland, R.
      (1998) Trends Biochem Sci 23: 242
    Organizational Affiliation: 

    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR AUTOANTIGEN SP100-BA95Homo sapiensMutation(s): 4 
Gene Names: SP100
UniProt & NIH Common Fund Data Resources
Find proteins for P23497 (Homo sapiens)
Explore P23497 
Go to UniProtKB:  P23497
PHAROS:  P23497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23497
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: ACCEPTABLE COVALENT GEOMETRY, FAVOURABLE NON-BOND ENERGY, FEWEST RESTRAINT VIOLATIONS, LOWEST OVERALL ENERGIES 
  • OLDERADO: 1H5P Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-28
    Changes: Database references, Source and taxonomy