It is possible that the following tetramer displays the features you seek:
https://www.rcsb.org/structure/6v1v
You will notice that this is P1. When I solved it, I had at first some
trouble recognizing why this molecule does not have a P4 (I am slow, I
guess) but then it dawned on me :) It displays one of the cutest symmetry
transitions that I've seen so far.
Artem
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On Thu, Jun 27, 2024 at 8:46 AM Andrew Lovering
wrote:
> Dear wise list,
>
>
>
> I have a question regarding protein oligomers that have multiple,
> differing axes of symmetry – stimulated by some perplexing but likely real
> Alphafold models.
>
>
>
> I think it’s the protein equivalent of this old chestnut:
> https://en.wikipedia.org/wiki/Three_utilities_problem
>
>
>
> Consider a trimeric fibre (perhaps collagen a good starting example) – it
> can have global 3-fold symmetry, and if it breaks from this, it is then
> able to “re-obey” this symmetry later on, but that axis is approximately
> the same as the starting one. I.e. a long winding rope with a kink in the
> middle, and the protein doesn’t have to do much to accommodate this.
>
>
>
> What happens when a long protein has multiple, dissimilar axes of
> symmetry? I.e. perhaps a trimer with the start and end on the same axis,
> but the middle domain sits ~90 degrees to this (and is also a 3-fold
> arrangement of chains A,B & C). I think I’d be correct in assuming that all
> 3 chains cannot have the same conformation – is this true?
>
> I’d argue that the protein has to unwind a little at the junctions and
> each chain takes a different path in space when migrating from axis 1> axis
> 2> back to axis 1? (think of 1 as up/down, 2 as left/right). This is
> because as each chain leaves the centre of mass of axis 1, it is a
> different distance away from the centre of mass of axis 2….?
>
>
>
> I hope that makes some sense!
>
>
>
> So my question is, does anyone have an example PDB that does something
> similar, and were they able to trace the different chains, demonstrating
> the different conformations.
>
>
>
> Thanks in advance - Andy
>
> --
>
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