Ribosomes and structure analysis

Protein crystallography:

Protein crystallography is the ideal tool to obtain accurate structural information, though it usually doesn't permit to capture the dynamics as well. This method reveals higher resolution than most alternative structure determination tools.

However, this requires first the crystallization of the protein, which sometimes turnes out to be a major obstacle. Crystals are build of well ordered elements, which diffract light (or hard xrays in this case) in a characteristic way. The characteristic diffraction pattern allows in principle to determine the precise location of each individual atom within the crystal, e.g. within the ribosomal particle. Sound easy, but that's unfortunately usually not the case ...

How does it really work ???
Just to get an idea, how xray crystallography works and how this method has been applied in ribosomal crystallography, we assembled some minimal information on protein crystallography. But don't expect a text book or tutorial, it just contains a crude description of some of the basic aspects ...

The mechanisms or functions of ribosomal protein synthesis are based on the structure and the dynamics - or conformational changes - of the ribosome, just like for any ordinary enzyme. To understand the function of the ribosome, one needs to know its structure, or better all the different structures corresponding to different functional states. The more accurate or detailed the structure becomes, the more accurate the understanding of the mechanism.

The ribosome is a so called ribo-nucleo-protein complex, which just means that its composed of rRNA and proteins. It always consists of two different ribosomal subunits, which are in case of the bacterial ribosome named 30S and 50S according to their sedimentation constant. Since sedimentation depends on the mass and the shape of a particle, 30S and 50S don't really represent the molecular mass. The 50S ribosomal subunit consists of 3000 nucleotides separated into 2 rRNA strands, 23S and 5S rRNA, and roughly 30 different ribosomal proteins. The 30S subunit is considerably smaller, with one rRNA chain and about 20 different proteins. Both subunits together comprise the 70S ribosome.

Bacterial ribosomes consist of 2 subunits:

(all other ribosomes as well, but we just concentrate on bacterial ribosomes)

30S

One rRNA chain (16S, grey)
and about 21 proteins assemble the 'small' or 30S ribosomal subunit.

50S

2 rRNA chains (5S, 23S; grey)
and about 33 proteins assemble the
'large' or 50S ribosomal subunit.

The structure of the 30S subunit from Thermus thermophilus (left) and the 50S subunit from Deinococcus radiodurans (right) are shown in pieces and in total. The structure of the 30S subunit has been solved by our group (we were first :0) ) (PubMed) and exactly at the same time (just 3 weeks later) by V.Ramakrishnan (PubMed). The 50S subunit has initially been determined by T.Steitz (PubMed), based on ribosomes of an archeal organism from the dead sea, Haloarcula marismortui. Roughly a year later, we were able to solve the structure of the 50S subunit from Deinococcus radiodurans (PubMed). This bacterium has many interesting features, but its not pathogenic. However, the ribosomes of this bacterial organism are extremly similar to ribosomes from pathogens, so that our structure provides an excellent tool to study the inhibitory activity of a large variety of antibiotics. Archeal ribosomes in contrast resemble more eukaryotic ribosomes, which has its own benefits, but is less suited to study ribosome-antibiotics interactions ...

Addendum 2008: Meanwhile 2 more high resolution structures of full 70S ribosomes exist. One of Thermus thermophilus in which the above mentioned 30S molecule is included and of Escherichia coli (better known as E.coli).

For protein biosynthesis with the help of several factors large and small subunit merge to a full ribosome, called 70S:

(simplified illustration)