Several years ago, we had an interesting case, where the molecule - a tetramer, did not possess the classical 222 or 4-fold symmetry. Rather, two monomers were related by a 2-fold, and other two monomers were related by yet another 2-fold. Ofcourse, the confirmation that it was indeed a tetramer was shown biochemically too! Our paper describing the "open" quaternary structure is:
Banerjee et al., Proc Natl Acad Sci USA (1994) v. 91, 227- 231. Shekhar On Fri, Dec 12, 2014 at 12:30 AM, Oganesyan, Vaheh <[email protected] > wrote: > 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. > > > > > > *Vaheh Oganesyan* > > *www.medimmune.com <http://www.medimmune.com>* > > > > *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of *Hay > Dvir > *Sent:* Thursday, December 11, 2014 12:04 PM > *To:* [email protected] > *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: [email protected] > <[email protected]>* > > ****************************************************************** > > > > > > > > On Dec 11, 2014, at 7:27 AM, Hay Dvir <[email protected]> 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 [email protected] > > Website http://tcsb.technion.ac.il > > > > > > > To the extent this electronic communication or any of its attachments > contain information that is not in the public domain, such information is > considered by MedImmune to be confidential and proprietary. This > communication is expected to be read and/or used only by the individual(s) > for whom it is intended. If you have received this electronic communication > in error, please reply to the sender advising of the error in transmission > and delete the original message and any accompanying documents from your > system immediately, without copying, reviewing or otherwise using them for > any purpose. Thank you for your cooperation. To the extent this electronic > communication or any of its attachments contain information that is not in > the public domain, such information is considered by MedImmune to be > confidential and proprietary. This communication is expected to be read > and/or used only by the individual(s) for whom it is intended. If you have > received this electronic communication in error, please reply to the sender > advising of the error in transmission and delete the original message and > any accompanying documents from your system immediately, without copying, > reviewing or otherwise using them for any purpose. Thank you for your > cooperation. > -- Shekhar C. Mande (शेखर चिं मांडे) Director, National Centre for Cell Science Ganeshkhind, Pune 411 007 Email: [email protected], [email protected] Phone: +91-20-25708121 Fax:+91-20-25692259
