JMS/Sandbox/msn2

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<applet load='AF-P33748-F1-model v4.pdb' size='400' frame='true' align='right' caption='' scene='10/1080095/Msn2/1'/>__NOTOC__
<applet load='AF-P33748-F1-model v4.pdb' size='400' frame='true' align='right' caption='' scene='10/1080095/Msn2/1'/>__NOTOC__
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=== Zinc Fingers ===
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Msn2 binds DNA via two C2H2 zinc finger domains located in the C-terminal region (residues 647-665 and 676-698).[4] These domains recognize the Stress Response Element (STRE) in the promoters of target genes.[1, 45] The AlphaFold model predicts these domains with high confidence (blue regions in the default view). Click the link to highlight these domains and the coordinating Zinc ions.
(<jmol><jmolLink>
(<jmol><jmolLink>
<script>
<script>
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# Reset and set base view (Grey cartoon + pLDDT colored wireframe atoms)
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select 647-665, 676-698; color magenta; backbone 0.7; wireframe 0.15;
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select all;
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select zn; spacefill 1.2; color cpk;
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cartoon on; color cartoon grey;
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selectionHalos ON; delay 1.5; selectionHalos OFF;
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wireframe 0.1; spacefill off;
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center selected; zoom 150;
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color atoms property bfactor range 0 100;
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color atoms property_bfactor >= 90 "#084594"; # Very High (>90) - Blue
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color atoms property_bfactor < 90 and property_bfactor >= 70 "#20BF55"; # Confident (70-90) - Green
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color atoms property_bfactor < 70 and property_bfactor >= 50 "#F9D142"; # Low (50-70) - Yellow
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color atoms property_bfactor < 50 "#E60A0A"; # Very Low (<50) - Red
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selectionHalos OFF;
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# Highlight Zinc Fingers (Residues 647-675, 676-703) [1, 2]
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select 647-675, 676-703; color backbone magenta; backbone 0.7;
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select zn; spacefill 1.2; color cpk; # Show Zinc ions
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# Highlight PKA-Regulated NLS (Residues 567-648) [3, 4]
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select 567-648; color backbone cyan; backbone 0.6;
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# Highlight NES region (Residues 283-293, near S288) [4]
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select 283-293; color backbone orange; backbone 0.6;
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# Highlight 9aaTAD Motif (Residues 261-269) [1, 2]
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select 261-269; color backbone lime; backbone 0.6; # Using lime green
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# Highlight Key PKA Phosphorylation Sites (S288, S582, S620, S625, S633) [3, 4]
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select 288, 582, 620, 625, 633; color atoms yellow; spacefill 100%; # Show sidechains as yellow spheres
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# Final view adjustments
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center protein; zoom 100;
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</script>
</script>
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<text>Show All Highlighted Features Simultaneously</text>
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<text>Highlight Zinc Fingers (DNA Binding: 647-665, 676-698)</text>
</jmolLink></jmol>)
</jmolLink></jmol>)
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The precise interaction with DNA likely involves specific residues within these fingers making contact with the STRE sequence.

Revision as of 13:38, 5 May 2025

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Zinc Fingers

Msn2 binds DNA via two C2H2 zinc finger domains located in the C-terminal region (residues 647-665 and 676-698).[4] These domains recognize the Stress Response Element (STRE) in the promoters of target genes.[1, 45] The AlphaFold model predicts these domains with high confidence (blue regions in the default view). Click the link to highlight these domains and the coordinating Zinc ions.

()

The precise interaction with DNA likely involves specific residues within these fingers making contact with the STRE sequence.

Proteopedia Page Contributors and Editors (what is this?)

Joseph M. Steinberger

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