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The first problem is that your GeoJSON file isn’t in degrees [longitude°, latitude°], otherwise known as EPSG:4326 or WGS 84. To convert your GeoJSON file to WGS 84, you first need to create a projection file, say albers.prj so that you can tell OGR what the source projection is.

+proj=aea +lat_1=52 +lat_2=64 +lat_0=0 +lon_0=105 +x_0=18500000 +y_0=0 +ellps=krass +units=m +towgs84=28,-130,-95,0,0,0,0 +no_defs

Then, “unproject” the GeoJSON file by converting it to WGS 84:

ogr2ogr -f GeoJSON -s_srs albers.prj -t_srs EPSG:4326 map_rus_wgs84_geo.json map_rus_geo.json

Now you can convert to TopoJSON in WGS 84, rather than projected coordinates. I’ve also taken the liberty of doing some simplification:

topojson -o map_rus_wgs84_topo.json -s 1e-7 -- russia=map_rus_wgs84_geo.json

The second problem is that your projection definition in D3 is incorrect. The d3.geo.albers projection has a default rotate and center that’s designed for a U.S.-centered map, so in addition to defining the center you’ll also need to override the default rotation. In fact, the +lon_0 (central meridian) projection parameter maps to the projection’s rotation, not the projection’s center. Giving:

var projection = d3.geo.albers()
    .rotate([-105, 0])
    .center([-10, 65])
    .parallels([52, 64])
    .translate([width / 2, height / 2]);

(I fudged with the center parameter to put Russia at the center of the viewport. You can compute this automatically if you prefer.) You should now see something like this:

Albers Siberia

It’s also possible to work with projected (Cartesian) coordinates in TopoJSON, and then define a d3.geo.path with a null (identity) projection, but I’ll leave that for a separate question.

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