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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?

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Chains are individual polypeptides that make up a multimeric protein complex.

I'm curious as to how they are first found and what causes them?

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.

As far as I understand, the protein backbone could be in any of several conformations and each conformation has a label? Is that correct?

Yes. The labels are assigned as per the reported conformation.

Is one chain more common than the other? What causes translation to produce different chains in this case? And finally, during the x-ray crystallography, how do they identify them when they grow the crystal?

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.

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Is one chain more common than the other? What causes translation to produce different chains in this case? And finally, during the x-ray crystallography, how do they identify them when they grow the crystal? Thank you again for your help! –  user1357015 Mar 21 at 14:58
    
edited the answer –  WYSIWYG Mar 22 at 5:35
    
Awesome, this helps a lot. So to be clear, your heterodimer of homodimers, that would be something like two chain A's bonded to two chain B's? Could it be completely different proteins bonded together? Last question: Also, let's pick a particular structure, say 3GFT in the PDB. There are 6 chains there. Are all 6 in the structure forming an ABCDEF heterodimer? What would be an example of a homodimer (I assume the same chain would be labeled twice?) Thank you again! –  user1357015 Mar 22 at 14:24
    
Slight addendum, it seems that 3GFT is a monomer, so how do the 6 chains come into play? –  user1357015 Mar 22 at 15:23
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