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