ETS family

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 code	Chain	Experimental method	Resolution, Å	DNA	Water	Protein	Species	Model	Chain renaimed
1BC7	c	X-ray	2,01	Yes	Yes	SAP-1	Homo sapiens	1	A
1BC8	c	X-ray	1,93	Yes	Yes	SAP-1	Homo sapiens	2	B
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
1FLI	a	NMR	N/A	No	No	Fli-1	Homo sapiens	6	F
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
1K6O	a	X-ray	3,19	Yes	No	SAP-1	Homo sapiens	11	K
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
1MDM	b	X-ray	2,8	Yes	No	ETS-1	Mus musculus	20	T
1PUE	e and f	X-ray	2,1	Yes	Yes	PU.1	Mus musculus	21 and 22	U and V
2STT	a	NMR	N/A	Yes	No	ETS-1	Homo sapiens	23	W
2STW	a	NMR	N/A	Yes	No	ETS-1	Homo sapiens	24	X
1YO5	c	X-ray	2	Yes	Yes	PDEF	Homo sapiens	25	Y
1WWX	a	NMR	N/A	No	No	ELF-5	Homo sapiens	26	Z
1R36	a	NMR	N/A	No	No	ETS-1	Mus musculus	27	[
2DAO	a	NMR	N/A	No	No	ETV-6	Homo sapiens	28	]

   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

   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.

   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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