In Mike Bostock’s original, the “z” axis is parallel to the North Pole. In Three.js, the default is “y” axis pointing “up”. Transform from original Cartesian axes to Three default by rotating 270 degrees about the X axis.
xThree = x = cos(φ)cos(λ) φ = latitude
zThree = - y = - cos(φ)sin(λ) λ = longitude
yThree = z = sin(φ)
That is: