Ask HN: HTML structure, semantics and Google ranking

Is there any well-sourced information available on how the HTML structure of a site may or may not affect its PageRank? My understanding of this is that as long a site is well organized, has a good site map and isn't doing anything sneaky (like hidden text, etc.) GA is cool.

We're currently working on a redesign project in an older CMS system, and one of the things we were looking to implement could only be accomplished by having the CMS add span tags inside heading tags. I've been told that this will negatively impact our site ranking.

My searches haven't turned up anything that would indicate this is something we should worry about, but any insights, experience or write ups I may have missed are appreciated.