|General information||Species distribution||Numeration assumed||Sequence conservation||3D conservation||Contacts with DNA|
For this study 20 PDB-entries containing coordinates of ETS domains were used.
These entries represent 10 proteins from two species: Homo sapiens
and Mus musculus. Due to the fact, that 8 of the PDB-entries taken into research
contain two examples of ETS domain, they were divided into separate PDB-files with only one
copy of ETS domain, other protein domains being removed. Finally 28 PDB-files were obtained
and taken into analysis. Complete information about the studied structures, including
the name of PDB-entry, the name of the chain representing ETS domain, experimental method,
resolution, presence of the DNA and water etc., is listed in the following table:
|PDB code||Chain||Experimental method||Resolution, Å||DNA||Water||Protein||Species||Model||Chain renaimed|
|1AWC||a||X-ray||2,15||Yes||Yes||GABP alpha||Mus musculus||3||C|
|1DUX||c and f||X-ray||2,1||Yes||Yes||Elk-1||Homo sapiens||4 and 5||D and E|
|1GVJ||a and b||X-ray||1,53||No||Yes||ETS-1||Homo sapiens||7 and 8||G and H|
|1HBX||g and h||X-ray||3,15||Yes||No||SAP-1||Homo sapiens||9 and 10||I and J|
|1K78||b and f||X-ray||2,25||Yes||Yes||ETS-1||Mus musculus||12 and 13||L and M|
|1K79||a and d||X-ray||2,4||Yes||Yes||ETS-1||Mus musculus||14 and 15||N and O|
|1K7A||a and d||X-ray||2,8||Yes||No||ETS-1||Mus musculus||16 and 17||P and Q|
|1MD0||a and b||X-ray||2||No||Yes||ETS-1||Mus musculus||18 and 19||R and S|
|1PUE||e and f||X-ray||2,1||Yes||Yes||PU.1||Mus musculus||21 and 22||U and V|
Then multiple alignment of these 28 structures was performed by means of SSM server. In the resulting PDB-file every copy of ETS domain was given a unique name (one latin letter) and number (number of the model with the structure). The protein sequences derived from PDB-files were aligned using GENEDOC. The picture of this alignment follows below:
The sequence alignment of all studied ETS domains
the gaps present in the alignment, all chains were renumbered so that after each
gap the numeration begins from a new number. Thus, all aligned residues of different
structures go under the same number and the gaps in the alignment do not put
the numeration out. The upper line of the alignment, called numbers shows
the starting points, where numeration begins from a new number.
The residue corresponding to the number in the upper line is located under the
first figure of the number. Thus, the residue 51 would be Ile, not Leu, which
would be 53.
The line called Aligned marks those residues which are generally aligned in the structural alignment. It is clear that the gaps in the sequence alignment correspond to the unaligned regions of the structural alignment, so the sequence alignment can be considered valid.
The lower line called 2nd_structure represents the trends of the AA residues to make &alpha -helix or &beta -sheet conformation.
The names of the sequences are colored according to their belonging to a certain protein. Thus, the sequences representing the same protein are of the same color.
Among all studied structures there are 20 that contain DNA chains, which
sequences were also aligned using GENEDOC. The alignment obtained reveals
the conservative trinucleotide core GGA, which is recognized by ETS domain
and is usually called EBS (ETS Binding Site). In order to unify all DNA chaines and
to provide possibility to correctly address them, they were also renumbered according
to the scheme below.
The alingment of DNA chains present in studied PDB-files and the scheme of DNA renumbering.
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