Ribosome Large Subunit

PDB file 1JJ2

Structure of the large ribosomal subunit of Haloarcula marismortui, including 28 of its 31 proteins plus the 23S and 5S rRNAs. This crystal structure was solved by D. J. Klein, T. M. Schmeing, P. B. Moore, & T. A. Steitz in 2001.

Suggested display options:

Select nucleic and display as sticks, with CPK color.

Select protein and display as cartoon, with color chain.
Drag to see the distribution of proteins.

Now select nucleic, and select hide selected. Drag to rotate.
Note
the extended structure of some proteins, and the way they protrude into the interior of the particle.
Question
: Why has it proved difficult to crystallize many of these proteins in isolation?
Look for the location of basic residues such as Arg and Lys.

Select a2486 and display as spacefill or sticks. This adenine residue is known to be located at the active site.
Select
protein and display as spacefill with color chain.
Question: Are there any proteins at the active site?

Now select nucleic, display as spacefill and color CPK.
Again select a2486 and change color to magenta.
Drag
to see the convoluted surface of the large ribosome subunit including the deep cleft where tRNAs bind near the active site adenine-2486.

Look for the tunnel through which nascent polypeptides emerge.
Hint: With proteins colored chain, a red and a blue protein line part of the tunnel near the outlet.

To get a closer look at the 5S rRNA, select all, and hide selected.
Then using mouse menus
select chain 9, and display as sticks, with color CPK.
What is the secondary structure of this small rRNA? Try also displaying as ribbons.

With nucleic displayed as wireframe, select hetero-ligand and display as spacefill with color CPK.
Question: Are there more inorganic cations or anions associated with the ribosome? Why?


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