Can someone please explain how different protein chains occur exactly? I'm not talking about the side chain, but the protein chain which is typically labelled as A,B,C etc in the PDB. I'm curious as to how they are first found and what causes them? As far as I understand, the protein backbone could be in any of several conformations and each conformation has a label? Is that correct?
Chains are individual polypeptides that make up a multimeric protein complex.
SDS-PAGE will resolve all the different chains (if they are different in molecular weight). Chains are products of translation (and some modifications such as clipping and/or other PTMs etc) and they assemble to form final protein complex.
Yes. The labels are assigned as per the reported conformation.
There can be different kinds of multimers. There can be homomultimer or a heteromultimer or a multimer of this configuration $(XX)_2$-$(YY)_2$ (a heterodimer of homodimers- just one arbitrary case) etc. Each chain is a polypeptide and is encoded by a distinct gene. It is possible that in a multimer there are more number of a certain chain than the other for e.g. $X_3$$Y$. This is not because $X$ is produced more then $Y$ but rather because of the way the multimer is assembled. In X-ray crystallography you basically get the arrangement of atoms. You can also understand which atom is what and similarly the termini can be found out. In any case people don't just proceed to crystallography without understanding the subunits and other biochemical properties.