This fact by itself is unusual to say the least (for me):
“ we have NO rotational symmetry (2, 3, or 4-fold) whatsoever between interacting monomers in the ASU or relating those built up by the crystallographic symmetry”
There might be several ways of choosing molecules to represent the asymmetric unit. Is it possible to find ones that are related? Say something like non-crystallographic translation (or pseudo translation) +
non-crystallographic rotation.
For long time I was thinking about such a possibility of having more than one molecule in au but no rotation or pst. May be I’ve missed but never found an evidence, nor can I explain why would that be impossible.
From: CCP4 bulletin board [mailto:[log in to unmask]]
On Behalf Of Hay Dvir
Sent: Thursday, December 11, 2014 12:04 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] asymmetric homotrimer in the asu
Dear Michael,
Thank you very much for the useful comments.
Indeed, we are of course looking at it biochemically, which isn't a clear cut so far..
As you pointed out it could be a monomer in solution, but the interface between monomers within this asymmetric trimer seems too extensive (compared to those responsible for the lattice packing) not to suspect a trimer as a solution assembly. PISA
suggested this asymmetric trimer as the most likely assembly but it falls into the grey region of their criteria (see attached pic.)
Since it's rare, we are interested to know of other similar reports, if any, to learn how they were resolved/concluded. I believe the case you describe is not similar, as we have
NO rotational symmetry (2, 3, or 4-fold) whatsoever between interacting monomers in the ASU or relating those built up by the crystallographic symmetry. Therefore I can't see how the space group information may help, but it is p212121 in case it helps
boosting your morning coffee experience with symmetry pondering ... :).
Cheers,
Hay
On Dec 11, 2014, at 3:47 PM, R. M. Garavito wrote:
Dear Hay,
And your point is? I am not trying to be snarky (although I am just starting my morning coffee), but to bring up the fact that CCP4BB readers need more info to comment on your case, like space group, local interactions, and how packed
is "tightly packed."
I have had two cases of "trimers," as my students initially called them, that were actually a dimer and a half. The "half" dimer had its mate in another ASU. Can it be a biological monomer that just happened to crystallize 3 monomers
to an ASU? Non-symmetric homo-oligomers are rare, but sadly cannot be absolutely confirmed by crystallography alone, but by good old biochemistry. The PISA website (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html)
can give you estimations of the strengths of the interfacial interactions, but they are mere estimates. What does gel filtration say or cross linking? Does it fit with the biology/biochemistry expected of this protein?
Anyway, have fun with your structure, but use a lot of skepticism in your interpretation. That will help you convince the reviewers.
Cheers,
Michael
****************************************************************
R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office: (517) 355-9724 Lab: (517) 353-9125
FAX: (517) 353-9334 Email: rm[log in to unmask]
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On Dec 11, 2014, at 7:27 AM, Hay Dvir <[log in to unmask]> wrote:
Dear all,
We have a structure of a rather tightly packed homotrimer protein in the ASU with no apparent crystallographic or non-crystallographic rotational symmetry between monomers.
Attempting to establish the biological assembly, we are very interested to hear about additional similar cases you might know of.
Thanks in advance,
Hay
---------------------------
Hay Dvir Ph. D.
Head Technion Center for Structural Biology
Technion Haifa 3200003, Israel
Tel: +(972)-77-887-1901
Fax: +(972)-77-887-1935
E-mail [log in to unmask]
Website
http://tcsb.technion.ac.il