Structure of the 50S ribosomal subunit from Deinococcus radiodurans
The bacterium Deinococcus radiodurans, also known as 'Conan the bacterium', has been discovered in the early 50's as a habitant of canned meat. The bug survives under extreme conditions, and feels even comfortable in rather unpleasant places like antartica. Its ability to withstand extreme stress made it a prime candidate in the Mars exploration project of NASA (hey folks, if extreme stress survival is all that's required, reserve me a ticket as well !!).
The bacteria are special in many respects, but most remarkably is probably the way, how it stores its genome. Deinococcus radiodurans contains several mostly identical copies of its chromosomes, which are distributed into four separated compartments. In case of massive radiation damage, the compartments unify, such that the destroyed genetic information can be restored from the redundant set of DNA fragments. The degree of destruction is further reduced through a compact, ring-like storage of the genetic code. This way, Deinococcus radiodurans survives a 1000 fold higher radiation dose than any other terrestrial organism.
Unfortunately, the resistance against ionizing radiation is not reflected by the crystals of the 50S subunit. However, the fact that the ribosomes could be crystallized at all, is certainly facilitated by the homogenity and stability of the ribosomes. And the ellipsoid crystals (see image) are still more stable than the 50S crystals from Haloarcula marismortui or the 30S crystals from Thermus thermophilus.
In most cases we need a few crystals to collected a complete dataset (i.e. sufficient amount of data of sufficient quality and resolution). Frequently, the radiation damage of the crystals is so severe, that already after a few exposures the diffraction starts to suffer, to largely varying extend. In case of 50S crystals from Haloarcula marismortui, this undesired effect is easily detectable by a strong increase of the cell dimensions and the internal disorder (or mosaicity) of the crystal.
Problems of this nature ultimatively limit the quality of the structure derived from the diffraction. For example the crystals of the 50S subunit from Deinococcus radiodurans diffract well beyond 3Å, but the structure we finally solved (how: check crystallography (sorry, so far only german)) has at best 3Å resolution. That's not bad at all, specially in comparison to electron microscopy, but rather poor compared to ultra-high (<1Å) resolution structures of some small proteins (small or big is really a matter of scale; even a small protein can still be a big challenge!). Most ribosome crystal structures end up with a similar resolution of roughly 3Å, with two noteworthy exceptions: the 50S structure of T. Steitz (2.4Å, PubMed) and the 70S strukture of H.Noller (~7Å, PubMed).
3Å, what does it actually mean ?? In other words, its 3*10-10m, oder 0.3nm. Just for comparison: a human cell has a size of 6.000-200.000nm, so its roughly 20.000-600.000 times larger than the details visible at 3Å. It shouldn't be too hard to imagine how much more detailed the structural information is, compared to a glance though an ordinary microscope.
The atomic bond length in a protein is (very) roughly 1.5Å, so its clear that at 3Å individual atoms are hardly resolved. However, individual rRNA nucleotides or side chains of amino acids are well visible, in theory. Even at much higher resolution, such details may get partially lost due to internal disorder, mobility or flexibility. Severe radiation damage or poor dataquality can make things even worse ... its never as good as it should be. Though some structures - and particularly some of the ribosome structures - lack the desired details, they still provide a wealth of information, which can facilitate - among other applications - the design of new drugs or inhibitors, as long as the limitations of a structure are clearly stated ...
Models of the 50S ribosome according to the PDB entry 1KC9, dressed up with some private knowledge. The structure has been described in: 'High Resolution Structure of the Large Ribosomal Subunit from a Mesophilic Eubacterium'. Joerg Harms et al., Cell, Nov.30, 2001: 107 (5), 679–688.
Facing the 30S subunit
+90o, view on the L7/12 stalk
50S ribosomal subunit from Deinococcus radiodurans by JMH (L1, L7/12 and L10 are inserted to complement the images, but have actually not been deposited)
View from the back, facing the solvent
+90o, view onto L1
The images present the structure of the 50S ribosomal subunit from four, 90o rotated, views. The presentation or orientation was choosen according to the first electron microscopy reconstructions of the 50S subunit. At that time, beginning of the 80's, the lack of detailed structural information, lead to a more phenomological description of the ribosome. The 5S region for example was termed Central Protuberance, the L7/L12 region became a stalk, and so on .... Remarkably is the distribution of ribosomal proteins: the interface towards the 30S subunit and also the catalytic core are essentially free of proteins, which therefore can't contribute to the enzymatic activity of the ribosome. This observation confirmed the old RNA-World hypothesis, that the rRNA is the fundamental, active part of the ribosome, and the proteins, which are mostly located on the back or solvent side of the 50S subunit, merely fine tune the process. Or in brief: the ribosome is a ribozyme ...
View facing the 30S subunit
+90o, view on the L7/12 stalk
50S from D. r., distribution of proteins and rRNA domains by JMH (L1, L7/12 and L10 are inserted to complement the images, but have actually not been deposited)
View from the back, facing the solvent
+90o, view onto L1
The secondary structure of 23S rRNA is traditionally divided into 6 domains. Unlike 16S rRNA, the domains appear much more nested and the division into domains doesn't really reflect their spatial distribution. For example domain 5 is splattered from the west to the far east (upper left image). The core region or peptidyl transferase centre is almost exclusively composed of domains 4 and 5 ....
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