"The proteins are stoichiometric"
Huh? What is the stoichiometry? I'm expecting a ratio here, like 1:1 or
some such.
I see two possibilities:
1) The two proteins are completely interchangeable in the structure.
2) The two proteins are not interchangeable, but are being
crystallographically averaged.
To differentiate, I would want more info, not necessarily crystallographic.
Do pure samples of either protein form the same structure (double hex ring)?
Does the stoichiometry of the complex ever vary?
Is there any data to suggest that the complex behaves any differently
than pure samples of either protein?
Do you have any non-crystallographic data on complex formation -
cross-linking results, etc. ?
On 12/16/16 11:45, Graham Robinson wrote:
Dear Crystallographers,
I have solved the structure of a complex, which is the average of its
component proteins. The problem is as follows:
The complex is composed of two proteins, which share 67%/84% sequence
identity/similarity in the resolvable region. The proteins are
stoichiometric (SDS-PAGE of the crystals), and form a dodecamer
composed of two hexameric rings, stacked on top of one another.
The crystals are H3. Analysis with Xtriage, Pointless, Aimless, Scala
do not find other space groups likely, and do not find any apparent
data pathologies. Data processing in H3 (to 1.9 A) is straight forward
(Rfactor/Rfree: 22.3%/26.4% using one of the proteins as MR model).
Attempts to solve the structure in other space groups (except P1)
fail, or produce meaninglessly poor statistics.
I have good anomalous data from isomorphous SeMet crystals, and the
anomalous difference density peaks for the Se are approximately
additive: anomalous peaks for positions where SeMet is unique to one
of the two proteins are about 1/2 the size of peaks common to both
proteins. This composite effect is apparent when the structure is
processed in P1 also.
Crystal contacts are not specific to either of the two proteins, and
so it appears that the crystal doesn't distinguish between up- and
down-orientations of the dodecameric rings. Therefore, each subunit in
the resulting structure is a composite of the two proteins.
Despite the occurrence of heteromeric rings in protein structures, I
have not been able to find a description of this problem in the
literature, nor the archives of the CCP4BB.
I am keen to hear from anyone who has observed similar things in
structures of their complexes, and how best to approach this problem.
Many thanks,
Graham Robinson
Postdoc, University of Geneva
Graham Robinson, Ph.D.
Fitzpatrick Group
Département de Botanique et Biologie Végétale
Université de Genève
30 Quai Ernest-Ansermet
CH-1211, Genève 4
T: +41 (0) 22/379.30.12
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
