ETS family

General information Species distribution Numeration assumed Sequence conservation 3D conservation Contacts with DNA

Numeration and designations assumed in this study

   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:

Information about the studied structures
PDB codeChainExperimental methodResolution, Å DNAWaterProtein SpeciesModelChain renaimed
1BC7cX-ray2,01Yes YesSAP-1Homo sapiens1A
1BC8cX-ray1,93Yes YesSAP-1Homo sapiens2B
1AWCaX-ray2,15Yes YesGABP alphaMus musculus3C
1DUXc and fX-ray2,1Yes YesElk-1Homo sapiens4 and 5D and E
1FLIaNMRN/ANo NoFli-1Homo sapiens6F
1GVJa and bX-ray1,53No YesETS-1Homo sapiens7 and 8G and H
1HBXg and hX-ray3,15Yes NoSAP-1Homo sapiens9 and 10I and J
1K6OaX-ray3,19Yes NoSAP-1Homo sapiens11K
1K78b and fX-ray2,25Yes YesETS-1Mus musculus12 and 13L and M
1K79a and dX-ray2,4Yes YesETS-1Mus musculus14 and 15N and O
1K7Aa and dX-ray2,8Yes NoETS-1Mus musculus16 and 17P and Q
1MD0a and bX-ray2No YesETS-1Mus musculus18 and 19R and S
1MDMbX-ray2,8Yes NoETS-1Mus musculus20T
1PUEe and fX-ray2,1Yes YesPU.1Mus musculus21 and 22U and V
2STTaNMRN/AYes NoETS-1Homo sapiens23W
2STWaNMRN/AYes NoETS-1Homo sapiens24X
1YO5cX-ray2Yes YesPDEFHomo sapiens25Y
1WWXaNMRN/ANo NoELF-5Homo sapiens26Z
1R36aNMRN/ANo NoETS-1Mus musculus27[
2DAOaNMRN/ANo NoETV-6Homo sapiens28]

Download ets.xls

   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 ETS alignment

   According to 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.

Download ets.msf

   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.

DNA alignment
EBS scheme

Download ets_dna.msf

© A.Grishin, A.Alexeevski, A.Karyagina, S.Spirin

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