An overview of the structures of protein-DNA complexes

By Nicholas M. Luscombe, S. E. Austin, Helen M. Berman, Janet M. Thornton. Genome Biology, 2000

640 citations recorded by the source corpus.

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e8291439ab47589e8c75ade51a9da901d66297a5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. M. V. van Dijk
2. Alexandre M. J. J. Bonvin
3. Rodrigo Vargas Honorato
4. Nicholas M. Luscombe
5. Jorge Roel‐Touris
6. Janet M. Thornton
7. Helen M. Berman
8. Wyeth W. Wasserman

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Boris Lenhard
4. Wyeth W. Wasserman
5. Albin Sandelin
6. David J. Arenillas
7. Rodrigo Vargas Honorato
8. Jorge Roel‐Touris

Citations in the corpus

• JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles (2009, background): “(43) and extended it to accommodate additional binding domain structures.”
• A census of human transcription factors: function, expression and evolution (2009, background): “Structural features The most common classification of TFs is based on the structure of their DNA-binding domain”
• Protein-RNA interactions: a structural analysis. (2001, background): “(1) Coat protein from Satellite tobacco mosaic virus (1A34); (2) bean pod mottle virus (middle component) (1BMV); (3) black beetle virus capsid protein (2BBV); (4) MS2 protein capsid (1ZDI); (5) HIV-1 nucleocapsid protein (1A1T); (6) aspartyl tRNA synthetase (1ASY); (7) glutaminyl tRNA synthetase (1”
• MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing (2019, background): “Those are composed of 26 binary, 16 ternary, 1 quaternary ( 2c5r ), and 1 pentameric ( 1ddn ) complexes covering all major types of interactions (Luscombe et al., 2000).”
• A protein–DNA docking benchmark (2008, methodology): “b The classification of the protein–DNA complexes in eight different groups according to the scheme of Luscombe et al. ( 6 ).”