Sandbox Reserved 49
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| - | <applet load='1IO4' size='300' frame='true' align='right' caption='The | + | <applet load='1IO4' size='300' frame='true' align='right' caption='The CBF1ab heterodimer binding to the Cs1 promoter.' |
scene='Sandbox_Reserved_49/Cbfdimer_domains_binding_dna/5' /> | scene='Sandbox_Reserved_49/Cbfdimer_domains_binding_dna/5' /> | ||
| - | Welcome to the Runx | + | Welcome to the Runx Structural Site. You will be amazed as you see the amazing dexterity of this molecule in regulating developmental processes.[Give general intro here].The depiction at right is of the DNA binding domains of Runx1 and CBFbeta binding to the CSR1 promoter. It is based on X-ray crystallography data and is therefore considered to be quite accurate. Note that only the binding domains are depicted so the two regions appear to be separate, while in fact if the entire proteins were present one could see that they actually constitute a heterodimer. The scene is interactive, so you can drag it into different perspectives,zoom in/out and measure atomic distances and angles.To see how the high degree of conservation in the Runx gene family translates into real functional structure, click on the following green words to see <scene name='Sandbox_Reserved_49/Cbfab_spacefill_conserved_bind/1'>conserved residues</scene> displayed, colored from white/yellow for non-conserved to purple for highly conserved. Note that the most highly conserved amino acids in both domains constitute the DNA binding regions. However, there are also notable pockets of highly conserved residues on the opposing surface of the Runt Domain. Mousing over these will identify the specific amino acids involved. Those that are not Gly or Pro can be indicative of active sites for events such as protein-protein interactions, for which Runx proteins are well-known. (NB!-Gly and Pro usually appear on protein surfaces when the structure simply needs to execute a fold since they are small and flexible, and are therefore usually not by themselves indicative of an active site.)Clicking on slab allows you to see a cross-section through the complex to better observe the conserved amino acids interacting with the DNA. |
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<applet load='1co1' size='300' frame='true' align='right' caption='Merged view of 10 different Runt domain configurations captured by NMR, helping to visualize the amount of flexibility inherent in the molecule. The regions more widely spread show more movement ''in vivo''. The protein backbone is colored from N(red)- to C(blue)- terminus.' /> | <applet load='1co1' size='300' frame='true' align='right' caption='Merged view of 10 different Runt domain configurations captured by NMR, helping to visualize the amount of flexibility inherent in the molecule. The regions more widely spread show more movement ''in vivo''. The protein backbone is colored from N(red)- to C(blue)- terminus.' /> | ||
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<scene name='Sandbox_Reserved_49/Cbfdimer_domains_binding_dna/2'>TextToBeDisplayed</scene> | <scene name='Sandbox_Reserved_49/Cbfdimer_domains_binding_dna/2'>TextToBeDisplayed</scene> | ||
Revision as of 09:18, 12 February 2010
| This Sandbox is Reserved from January 7, 2011, through March 31, 2011 for use in the workshop Practical Protein 3D Structure Visualization & Structural Bioinformatics taught by Eric Martz at the University of Massachusetts, Amherst. This reservation includes Sandbox Reserved 41 through Sandbox Reserved 60. Dates, Location, Syllabus: Workshops.MolviZ.Org. |
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Welcome to the Runx Structural Site. You will be amazed as you see the amazing dexterity of this molecule in regulating developmental processes.[Give general intro here].The depiction at right is of the DNA binding domains of Runx1 and CBFbeta binding to the CSR1 promoter. It is based on X-ray crystallography data and is therefore considered to be quite accurate. Note that only the binding domains are depicted so the two regions appear to be separate, while in fact if the entire proteins were present one could see that they actually constitute a heterodimer. The scene is interactive, so you can drag it into different perspectives,zoom in/out and measure atomic distances and angles.To see how the high degree of conservation in the Runx gene family translates into real functional structure, click on the following green words to see displayed, colored from white/yellow for non-conserved to purple for highly conserved. Note that the most highly conserved amino acids in both domains constitute the DNA binding regions. However, there are also notable pockets of highly conserved residues on the opposing surface of the Runt Domain. Mousing over these will identify the specific amino acids involved. Those that are not Gly or Pro can be indicative of active sites for events such as protein-protein interactions, for which Runx proteins are well-known. (NB!-Gly and Pro usually appear on protein surfaces when the structure simply needs to execute a fold since they are small and flexible, and are therefore usually not by themselves indicative of an active site.)Clicking on slab allows you to see a cross-section through the complex to better observe the conserved amino acids interacting with the DNA.
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