ETS family

Conserved features of ETS 3D structure

   28 3D-structures of ETS domain were superimposed by means of SSM server with the following results:

Multiple alignment results Protein & species Structure RMSD Q-score PDEF H. sapiens 1yo5:C 0.8654 0.7448 SAP-1 H. sapiens 1bc7:C 0.5030 0.7426 1bc8:C 0.5221 0.7410 1k6o:A 0.5530 0.7715 1hbx:G 1.0468 0.5651 1hbx:H 0.7236 0.6156 GABP alpha M. musculus 1awc:A 0.7442 0.6080 Elk-1 H. sapiens 1dux:C 1.0680 0.7327 1dux:F 1.0648 0.7332 ETS-1 H. sapiens 2stt:A 1.9331 0.5226 2stw:A 2.0057 0.5111 1gvj:A 0.5813 0.4853 1gvj:B 0.6044 0.4673 PU.1 M. musculus 1pue:E 1.1052 0.7104 1pue:F 1.2193 0.6847 ETS-1 M. musculus 1k79:A 0.5982 0.6566 1k79:D 0.5374 0.6615 1mdm:B 0.5254 0.5340 1k7a:A 0.5008 0.6642 1k7a:D 0.5350 0.6616 1k78:B 0.6695 0.6631 1k78:F 0.5652 0.6657 1md0:A 0.7115 0.4871 1md0:B 0.7085 0.4873 1r36:A 1.4473 0.4114 Fli-5 H. sapiens 1fli:A 1.9811 0.5045 ELF-5 H. sapiens 1wwx:A 1.1006 0.5848 ETV-6 H. sapiens 2dao:A 1.1797 0.5211 Overall RMSD 1.4671 Overall Q-score 0.3240

Here pictures of superposed structures are represented. The first picture shows the whole ETS domain, while the others show particular secondary structure elements to provide possibility of observing them more clearly. Superposed structures of the whole ETS domain   Superposed helix#1 and helix#2   Superposed helix#3   Superposed beta-sheet      As it is seen on the pictures, most deviations are observed between second structure elements and in loops, most insertions in amino acid sequences being also there. Helices and sheets seem to have more conservative 3D structure, which is especially obvious for the recognition helix #3, where the most deflected chains are the ones without DNA. Download ets.ent

   By means of CluD the hydrophobic core of every structure was analyzed. Atoms found in the core of 7 or more proteins were assumed conservative and more or less important for forming protein 3D structure.

List of atoms engaged in conserved hydrophobic core residue.atom Number of proteins residue.atom Number of proteins 52.cb 8 257.cb 10 53.cb 10 260.cb 9 54.cb 10 261.cb 8 55.cb 10 302.cb 8 phe56.cb 10 met305.cb 10 phe56.cz 8 met305.ce 10 57.cb 10 met305.sd 10 58.cb 8 307.cb 10 60.cb 10 309.cb 9 61.cb 10 310.cb 10 101.cb 8 314.cb 10 104.cb 9 315.cb 8 105.cb 10 317.cb 10 107.cb 10 320.cb 7 phe202.cb 10 322.cb 10 phe202.cz 10 323.cb 10 204.cb 10 325.cb 10 206.cb 9 352.cb 9 207.cb 8 353.cb 10 252.cb 8 355.cb 10 253.cb 10 phe357.cb 10 254.cb 10 phe357.cz 9 256.cb 9 361.cb 8

Totally 41 residues are engaged in the conserved hydrophobic core, 31 of them are at the same time conserved according to Pfam alignment. 21 of those residues do not make any contacts to DNA, thus being important only due to their role in hydrophobic core of the ETS domain.

Download core.xls

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