Blogging a crystal structure a day in 2014


Contributed by

Brett Collins

The machine of life – the structure of the Ribosome

What does it look like?

The image was generated using the molecular graphics software ccp4mg.

The image was generated using the molecular graphics software ccp4mg.

The atomic resolution structure of the large ribosomal subunit at 2.4 Å Resolution (PDB ID 1FFK, Ban et al., Science, 2000). Shown in grey are the RNA molecules of the ribosomal subunit, and ribosomal proteins are shown in different colours.

What is it?

The ribosome is the complex molecular machine that is found in all living cells. Peptide-bond formation and protein synthesis by the ribosome is essential to all life on earth. Ribsomes of every species are composed of two unequally sized subunits named, imaginatively, the large and small subunits.

In 2000 the structure of ribosomal subunits were finally revealed at atomic resolution through crystal structures determined in the labs of Ada Yonath, Tom Steitz and Venki Ramakrishnan. This work and work from others in the intervening years have pushed the envelope of crystal structure determination of enormous biological macromolecular complexes.

It remains one of the largest structures of an asymmetric macromolecule determined to date. The structure shown here is the original 2.4 Å resolution structure of the large ribosomal subunit from Haloarcula marismortui, which catalyzes peptide bond formation and binds initiation, termination, and elongation factors. It includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins.

The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.

Where did the structure come from? This structure was determined by the lab of Tom Steitz. You can view it at and read more about it in

Tags: life   ribosome   complex   biological   biology