Unless you are playing Pacific 1940 by itself. Then San Francisco is considered the US Capital and if Japan manages to capture the Western United States, they will get to plunder the US treasury like if they captured any other capital.
If you are playing Global 1940, then Noll is right. San Francisco becomes a Victory City and Washington DC is the US Capital.
I like to use a house rule that provides a secondary capital for the US. Some people like to play it where if London gets captured by the Axis, then the British government transfers to Ottawa so Britain can keep fighting on. I like to do the same thing with the US, where if Washington is captured, the US Government transfers to San Francisco. You would think if the Axis managed to capture the Eastern US, the game would pretty much be over. However, if it was a very costly battle and the Axis barely managed to take it with just a couple of units left in the fight, America could get it back by launching an attack from the Western US.
The US and England are the only ones I do that for. The other allies are too small to have a secondary capital. The Axis are dictatorships that would not likely want to spread their power to anywhere but the main seat of government. Russia, while technically an Ally, is really the same as the Axis politically, so they only get the single capital as well.