Buying a car is, by all accounts, a huge pain. The point of Boston-baesd Mojo Motors is to introduce a trusted intermediary to help shoppers sort through deals, compare options, receive alerts and more. The company announced today that it has raised a $3 million Series A round led by Atlas Venture and joined by existing investors NextView Ventures and RPM Ventures, according to TechCrunch.

As opposed to sites like Cars.com, Mojo is aiming to offer a dramatically more customized experience, as we described in a piece on their launch last year. As my colleague wrote then:

Just how big is Mojo’s market? In 2009, over 35 million used vehicles were sold in the US alone, with sales up even more in 2010 thanks to the recession.

The site is free to join for buyers and charges sellers a $350 fee for any sales they actually make through the site. Balancing out the power relationship between buyer and seller has clear value for the former, but it will be interesting to see how auto sellers react.

[UPDATE: 10:13am: This article mistakenly said that the $350 charge was for users. It is only for dealers.]