DOI: 10.6084/m9.figshare.1132729
title: 3D models from "Human TFIID binds to core promoter DNA in a reorganized structural state"

description: <em>3D models from the publication: </em>
<strong>Human TFIID binds to core promoter DNA in a reorganized structural state</strong>
Michael A. Cianfrocco, George A. Kassavetis, Patricia Grob, Jie Fang, Tamar Juven-Gershon, James T. Kadonaga, and Eva Nogales
<em>Cell. Jan 17, 2013; 152(1-2): 120–131.</em>
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To create specific figures from the publication, first download the appropriate files:
1) Download the .zip archived file <em>Cianfrocco_et_al_2013_3D_Models.zip</em>.
2) Download and install the latest version of <em>UCSF Chimera.</em>
3) Within Chimera, go to<em> File &gt; Restore Session</em>, selecting the file <em>Figures_Chimera_Session.py</em> from the unzipped folder from step #1.
4) Once opened, Chimera will display an interactive session showing <em>Example_Snapshot.png.</em>
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After Chimera is installed and the .zip file is uncompressed, following these steps for generating specific parts of the figures. Each set of instructions assume that you are starting from provided Chimera session file: 
<strong>Figure 3C: </strong>
<strong>1)</strong><em> Tools &gt; Volume Data &gt; Volume Viewer</em>
<strong>2) </strong>On the new window, click on <em>Data &gt; IID-IIA-SCP rearranged</em>
<strong>3) </strong>Now select 'surface' from the style choices. 
<strong>4)</strong> Go to the model panel:<em> Favorites &gt; Model Panel</em>
<strong>5) </strong>Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>Figure 3D:</strong>
<strong>1)</strong> Go to the model panel: <em>Favorites &gt; Model Panel</em>
<strong>2) </strong>Uncheck box for<em> IID-IIA-SCP rearranged</em>
<strong>3)</strong> Check box for <em>TFIID rearranged</em>
<strong>4)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>Figure 3E:</strong>
<strong>1)</strong> Go to the model panel: <em>Favorites &gt; Model Panel</em>
<strong>2)</strong> Uncheck box for <em>IID-IIA-SCP rearranged</em>
<strong>3)</strong> Check box for <em>IID-IIA-SCP canonical</em>
<strong>4)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>Figure 3F:</strong>
<strong>1) </strong>Go to the model panel: <em>Favorites &gt; Model Panel</em>
<strong>2)</strong> Uncheck box for <em>IID-IIA-SCP rearranged</em>
<strong>3)</strong> Check box for <em>TFIID canonical</em>
<strong>4)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>Figure 4A:</strong>
<strong>1)</strong> Go to the model panel: <em>Favorites &gt; Model Panel</em>
<strong>2)</strong> Uncheck box for <em>IID-IIA-SCP rearranged</em>
<strong>3)</strong> Check box for <em>IID-IIA-SCP(+30) rearranged</em>
<strong>4)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>Figure 6A & B: Core promoter elements</strong>
<strong>1) </strong>Open Chimera and load session.
<strong>Figure 6A & B: DNase I footprint</strong>
<strong>1)</strong> Go to the model panel: <em>Favorites &gt; Model Panel</em>
<strong>2)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>3)</strong> Check boxes next to <em>DNase IID-IIA-SCP</em> and <em>DNase IID-IIA-SCP surface</em>
<strong>Figure 6A & B: MPE-Fe footprint</strong>
<strong>1)</strong> Go to the model panel: <em>Favorites &gt; Model Panel</em>
<em></em><strong>2)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<em></em><strong>3)</strong> Check boxes next to <em>MPE_Fe_IID_IIA_SCP</em> and <em>Surface of MPE_Fe_IID_IIA_SCP</em>
<strong>Figure 6C:</strong>
<strong>1) </strong>Go to the model panel:<em> Favorites &gt; Model Panel</em>
<strong>2)  </strong>Uncheck the box next to <em>Surface of SCP30_promoter</em>
<strong>3)</strong> Check boxes next to<em> PDB: 1NVP </em>and<em> PDB: 1VOL.</em>
<strong>Figure S6B:</strong>
<strong>1)</strong> Go to the model panel:<em> Favorites &gt; Model Panel</em>
<em></em><strong>2)</strong> Uncheck box for <em>IID-IIA-SCP rearranged</em>
<em></em><strong>3)</strong> Check box for <em>IID-IIA-SCP(mTATA) rearranged</em>
<em></em><strong>4)</strong> Uncheck the boxes next to <em>SCP30_promoter</em> and <em>Surface of SCP30_promoter</em>
<strong>Supplemental Movie 2: </strong><strong>Segmented 3D maps of TFIID</strong>
<strong>1)</strong> Go to the model panel: <em>Favorites &gt; Model Panel</em>
<strong>2)</strong> Uncheck box for <em>IID-IIA-SCP rearranged</em>
Then, check the box for the model that you would like shown:
<em>TFIID canonical, lobe A only: </em>Lobe A (extracted from canonical IID alone)
<em>TFIID canonical, BC core only: </em>BC core (extracted from canonical IID alone)
<em>TFIID rearranged, lobe A only: </em>Lobe A (extracted from rearranged IID alone)
<em>TFIID rearranged, BC core only: </em>BC core (extracted from rearranged IID alone)
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<strong>File information:</strong>
<em>EMD-2282.spi -</em> TFIID-IIA-SCP, rearranged
<em>EMD-2283.spi - </em>TFIID-IIA-SCP, canonical
<em>EMD-2284.spi - </em>holoTFIID, rearranged
<em>EMD-2287.spi -</em> holoTFIID, canonical
<em>Figure.png -</em> Example snapshot of opened session
<em>Figures_Chimera_Session.py -</em> Chimera session file 
<em>IID_IIA_SCP+30_rearranged.spi -</em> 3D model for TFIID-IIA-SCP(+30) (Figure 4A)
<em>IID_IIA_SCPmTATA_rearranged.spi - </em>3D model for TFIID-TFIIA-SCP(mTATA) (Figure S6B)
<em>SCP1_30.pdb -</em> PDB coordinate file for SCP(+30) sequence
<em>holoTFIID_canonical_BC.mrc -</em> BC core from TFIID alone (canonical)
<em>holoTFIID_canonical_lobeA.mrc -</em> lobe A from TFIID alone (canonical)
<em>holoTFIID_rearranged_BC.mrc -</em> BC core from TFIID alone (rearranged)
<em>holoTFIID_rearranged_lobeA.mrc -</em> lobe A from TFIID alone (rearranged)
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