Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.05 kDa 
• Atom Count: 774 
• Residue Count: 95 
• Unique protein chains: 1

1H5P

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

• DOI: 10.2210/pdb1H5P/pdb
• BMRB: 5558

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-05-24 Released: 2001-07-06 
• Deposition Author(s): Bottomley, M.J., Liu, Z., Collard, M.W., Huggenvik, J.I., Gibson, T.J., Sattler, M.

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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 

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

• PubMed: 11427895 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR AUTOANTIGEN SP100-B	A	95	Homo sapiens	Mutation(s): 4  Gene Names: SP100
Find proteins for P23497 (Homo sapiens) Explore P23497  Go to UniProtKB:  P23497
NIH Common Fund Data Resources
PHAROS  P23497

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

Entry History 

Deposition Data

• Deposited Date: 2001-05-24 
• Released Date: 2001-07-06 
Deposition Author(s): Bottomley, M.J., Liu, Z., Collard, M.W., Huggenvik, J.I., Gibson, T.J., Sattler, M.

Revision History 

• 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