The putative locations of the DNA-binding domain (DBD) and the helices of the ligand-binding domain (LBD) are indicated and numbered in the multiple sequence alignments. In the HSSP format, the numbering is detailed in the 2nd column. In the 2 Mview-like formats, the numbering is above the consensus sequence (only round numbers are indicated) .
The DBD is numbered from D001 to D066, D068, or D070 (depending of the family), the 2 last residues being the conserved 'GM'.
The helices of the LBD are also annotated (Folkertsma et al., in preparation). We have combined structural information (have a look at Simon's structural alignment), multiple sequence alignments and the Predict Protein server (B. Rost et al., PHD, CUBIC, NY) in order to determine the position and length of the helices.
Residue numbering of the helices of the LBD
Each helix is numbered with a 3- or 4-digit numbering (3 for helices 1 to 9; 4 for helices 10 to 12); the 1st digit(s) corresponds to the helix number. The 2 last digits of the most conserved position (among all the receptors) is '50'. For example, the 'D' of the 'DQ' motif in helix 4 is numbered 450 (and the following Q '451').
|1||137 - 156||150 - E||not always present|
|2||not (yet) indicated|
|3||328 - 353||350 - A (WAK)|
|4||447 - 458||450 - D (DQ)|
|5||548 - 560||550 - E|
|6||647 - 653||650 - L/A/G/M/V||not always present|
|7||736 - 751||750 - L/M||E at pos.745 only present in families 2 (RXR) and 5 (FTZ)|
|8||848 - 859||850 - E|
|9||936 - 958||950 - L|
|10-11||1038 - 1061||1050 - L (LR)||helices 10 and 11 are continuous|
|12||1245 - 1252||1250 - E (EML)||not always indicated|
Other 2D structures: