October 2000 Molecule of the Month by David Goodsell
Keywords: protein translation, protein synthesis, RNA structure, ribosomal RNA, ribonucleoprotein complex
The Protein Factory
Protein synthesis is the major task performed by living cells. For instance, roughly one third of the molecules in a typical bacterial cell are dedicated to this central task. Protein synthesis is a complex process involving many molecular machines. You can look at many of these molecules in the PDB, including DNA, DNA polymerases, and RNA polymerases; a host of repressors, DNA repair enzymes, topoisomerases, and histones; tRNA and acyl-tRNA synthetases; and molecular chaperones. This month, for the first time, you can also look at the factory of protein synthesis in atomic detail.
An Elusive Structure
The ribosome has been under the scrutiny of scientists for decades. Electron microscopy has yielded an increasingly detailed
view over the years, defining the overall shape of individual ribosomes and differences in this shape for ribosomes from
different species, More recently, detailed electron micrograph reconstructions have studied the interaction or ribosomes
with messenger RNA, transfer RNA and the protein elongation factors. This legacy of morphological work lays the groundwork
on which the atomic structures may be understood.
Ribosomes are composed of two subunits: a large subunit, shown on the right, and a small subunit, shown on the left. Of course, the term "small" is used in a relative sense here: both the large and the small subunits are huge compared to a typical protein. Both subunits are composed of long strands of RNA, shown here in orange and yellow, dotted with protein chains, shown in blue. When synthesizing a new protein, the two subunits lock together with a messenger RNA trapped in the space between. The ribosome then walks down the messenger RNA three nucleotides at a time, building a new protein piece-by-piece.
The Large Subunit
The structure of the large subunit is available in PDB entries
The large subunit contains the active site of the ribosome: the site that creates the new
peptide bonds when proteins are synthesized. In this view, the messenger RNA would run
horizontally in the groove across the middle. This structure, along with several other
structures with inhibitors bound, provide strong evidence that the ribosome is a
ribozyme. Enzymes typically use amino acids to catalyze chemical reactions,
but the ribosome appears to use an adenine RNA nucleotide to perform its synthetic task.
This adenine is colored green in the figure (we'll look at this more closely later).
The large subunit is composed of two RNA strands: a long one colored orange and a shorter one colored yellow. Dozens of proteins bind on the surface of the ribosome. Many have long, snaky tails that extend into the body of the ribosome, gluing the RNA strands into their proper shape. Several of the proteins were not seen in this crystallographic structure, perhaps because they are too flexible. Approximate shapes for these proteins, which form two prominent stalks commonly used as landmarks in electron micrographs, are indicated here in light blue.
The Small Subunit
The structure of the small subunit is available in the PDB entries
The small subunit is in charge of information flow during protein synthesis. It initially finds
a messenger RNA strand and, after combining with a large subunit, ensures that each codon in the
message is paired with the anticodon in the proper transfer RNA. The messenger RNA is thought
to enter through a small hole (seen here on the left side of the molecule) and then extend up
into the "decoding center" in the cleft between the "head" at top and
the "body" at the bottom. The messenger RNA does not have to thread through this
hole like a needle, however, because the hole is actually formed by a loop of the ribosomal RNA,
which can open like a latch to admit the messenger.
To download an animated movie of this subunit, click on the molecule or click here.
Exploring the Structures
Before jumping into these structures, be prepared. Both the large subunit
and the small subunit are enormous complexes with many atoms: the structure of the large
subunit in PDB entry 1ffk
contains over 64,000 atoms, even though the authors chose to release only alpha carbon
positions for the proteins, and the small subunit structure (1fka), also with partial structures for
the proteins, contains almost 35,000 atoms. Many interactive display programs become
very sluggish when working on structures this large.
The picture shown here shows the proposed active site in the large ribosomal subunit. Adenine 2486 is thought to perform the synthesis reaction, at the location indicated by the yellow arrow. The two guanines shown on the left and the potassium ion shown in green serve to activate this adenine through a series of hydrogen bonds, shown in light blue. This picture was created with RasMol. You can create a similar picture by turning off display of the whole structure and then selectively displaying A2486, A2485, G2102, and G2482.
© 2015 David Goodsell & RCSB Protein Data Bank