To hide it with javascript, first assign a behaviorID to the extender. Then use the following code to close it.
your popup extender tag:
<ajaxToolkit:PopupControlExtender ID="PopupControlExtender1" BehaviorID="pop" runat="server" PopupControlID="Panel1" TargetControlID="Button1">
</ajaxToolkit:PopupControlExtender>
call hide() functipon in onChange event of your drop down.
function hide()
{
var e = document.getElementById("dropdown_Id");
var strUser = e.options[e.selectedIndex].value;
if(strUser!='')
{
var bh = $find("pop");
bh.hidePopup();
}
else
{
return false;
}
}