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 - Cosmic Cats approve of this message On Thu, Jun 27, 2024 at 8:46 AM Andrew Lovering <a.lover...@bham.ac.uk> 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 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
