Primary Citation PubMed: 18381292
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.
(2014) Nucleic Acids Res 42
PubMed: 25114055 | PubMedCentral: PMC4176381 | DOI: 10.1093/nar/gku730
MATERIALS AND METHODS Preparation of the starting structure The starting structure for the analysis was mouse CSL bound to DNA (HES-1 ( hairy and enhancer of split-1 ) site 5’-TGTGGGAA-3 ... 9;; PDB code 3BRG, resolution 2.2 Å), which contains all of the CSL conserved features but lacks the variable N-terminal residues (52 residues in mouse).
For the modeling experiments, mutations were introduced into the CSL structure, bound to the consensus TGTGGGAA DNA sequence (PDB ID: 3BRG), using MODELLER 9v8.
Starting from the X-ray structure where CSL binds its highest-affinity DNA motif comprised of eight nucleotides CGTGGGAA (PDB code 3BRG ( 17 ), Figure 1B ), all 4 8 permutations of an 8-nt motif were tested and the resulting 65 536 relative binding energies calculated (Figure 1A ).
The unbound structure of the protein was created from the 3BRG crystallographic structure of the protein bound to DNA, by stripping DNA from the complex followed by optimization (energy minimization) in implicit solvent.
Publication Year: 2014
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.