3D Structure of **RETINOBLASTOMA**

CPK Color Scheme
C O N P S



Now for a brief tutorial of the structure and interactions of the Retinoblastoma protein:

The retinoblastoma protein (Rb) is crucial in cell cycle regulation, more specifically the transition of a cell into S phase from G1. It does this by forming a chemical bridge through the use of its Alpha/Beta Pocket and sequestering together HDAC (histone deacetylase) and E2F (transcriptional activator) to prevent the binding of transciption factors to chromatin and thus prevent cell proliferation. Thus, one can also see the apparent function and need of the Rb protein as a global anti-oncogene as it functions in every cell. This tutorial will also briefly adress the interraction of an oncoprotein with Rb and the mechanism behind the formation of tumors associated with the E7 protein and cervical cancer.

Click this button to reset the protein to its original view. Click here.

The first logical step would be to view the protein as its two basic sub-groups: the alpha (blue) and beta (green) chains of the A/B pocket. The Alpha Sub-Unit consists of a cyclin fold, three-helix bundle with two additional packing helices on two sides to yield a five helix core motif. The Beta sub-unit consists of precisely the same thing. It is possibile to see these core helices here. Red represents the helices of the Alpha pocket, green represents the helices of the Beta pocket, and yellow represents helices involved in mainly connecting the two pockets that interract with both sub-units.

The joining of these two sub-units is made possible through an interface core. It is comprised of interactions between seven helices to form a hydrophobic core of about 20 side chains. A better view of the presence of these side chains and their congregation towards the middle of the molecule is available here. The Hydrophobic side chains (thicker stick forms: yellow and orange involved in A/B interface connected by a thin wire frame protein back bone) arise from the helical structures (gray) in the main sub-units and form a sturdy core by which the two units can be bound. Additional interface support is provided by a network of hydrogen bonds formed between side chains of the Rb protein that can be seen here represented by dotted lines throughout the protein, though this view is mainly of the interface The overall effect due to the bonding and cohesiveness that is generated in the pocket is similar to a connective large globular protein that can be easily visualised here.The interface unit (yellow and orange) is connecting the two sub-units (red and green).

The Beta sub-unit is used in the functioning of Rb to bind transcriptional activators such as E2F. This occurs in a shallow grove that is formed through the interaction of three of the Beta sub units helices that are easily visible here in dark orange. Click here for a view of the indentation (B-Shallow Groove) created by these structures. The Alpha sub-unit is indicated in gray.

However, the retinoblastoma protein can be affected by the invasion of an oncoprotein provided by a virus such as HPV, a cause of cervical canver. This protein is known as E7 and it competes with transcriptional activators at the Beta Shallow Groove mentioned in the last section. Click here for a view of the oncoprotein nestled into the groove. It is indicated in blue, the alpha unit is indicated in yellow, and the beta shallow groove is outlined once again by dark orange with the accompanying beta sub-unit helices being indicated by light orange.

The E7 protein accomplishes this through use of its LXCXE peptide domain that makes intermolecular contacts with the Beta sub-unit (leu 22, cys 24, glu 26, and leu 28). These are indicated more clearly by clicking here: leu is indicated by purple, cys is indicated by light blue, glue is indicated by yellow, the alpha sub-unit is indicated by white and the beta sub-unit's shallow groove area is indicated by transparent green helices. Here is a frontal view of the oncoprotein binding to the Beta sub-unit without the presence of the Alpha sub-unit. This is dangerous news for the Rb protein as most oncoproteins also use the LXCXE binding motif and can thus readily affix themselves and affect the proteins function and confirmation. Additionally, it could compete with E2F in a cell to prevent it from being regulated. If it causes the protein to release either the HDAC or transcriptional activator such as E2F, serious problems with the mechanism of the cell cycle will arise. These problems are what gives rise to tumors and subsequently malignant cancer.

It is my hope that this tutorial in some way aided in your understanding of the structure and functioning of retinoblastoma as well as its importance.


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References



Brehm, Alexander et al. 1998. Retinoblastoma protein recruits histone deacetylase to repress transcription. Nature 391:597-601

Lee, Jie-Oh et all. 1998. Structure of the retinoblastoma tumour-suppressor pocket domain bound to a peptide from HPV E7. Nature 391:859-865