JMS/Sandbox/msn2 1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (20:18, 19 May 2025) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Your Heading Here (maybe something like 'Structure')==
<StructureSection size='340' side='right' caption='Caption for this structure' scene='10/1080617/Msn2/1'>
<StructureSection size='340' side='right' caption='Caption for this structure' scene='10/1080617/Msn2/1'>
-
<scene name='10/1080617/Msn2/1'>initial view</scene>
+
<jmol><jmolButton><script>select all; spacefill on; cartoon off;</script><text>Show Surface Representation</text></jmolButton></jmol>
-
</StructureSection>
 
-
<jmol>
 
-
<jmolButton>
 
-
<script>
 
-
select all; cartoon on; color gray;
 
-
select 270-300; cartoon off; spacefill 180; color magenta;
 
-
select 573-590 or 620-639; cartoon off; spacefill 180; color lime;
 
-
select 642-704; cartoon off; spacefill 180; color orange;
 
-
</script>
 
-
<text>show entire protein in gray cartoon, NES in magenta, NLS in lime, DBD in orange</text>
 
-
</jmolButton>
 
-
</jmol>
 
-
The 3D structure shown is a predicted model from AlphaFold, providing insights into Msn2’s fold, as no experimental structures are currently available. The model is based on the 704-amino-acid sequence from [UniProt: P33748](https://www.uniprot.org/uniprotkb/P33748/entry).
+
<jmol><jmolButton><script>select all; cartoon; color chain; wireframe off; spacefill off; labels off; set ambientPercent 85; set diffusePercent 85;</script><text>Show Overall Structure</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; spin on; wireframe off; spacefill off;</script><text>Rotate Structure</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; spin off; cartoon; color chain; select 647-665; color red; wireframe off; spacefill off; zoom 400; center selected;</script><text>Zoom to Zinc Finger 1 (647-665)</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; select 676-698; color blue; wireframe off; spacefill off; zoom 400; center selected;</script><text>Zoom to Zinc Finger 2 (676-698)</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; select 237-327; color green; wireframe off; spacefill off; zoom 200; center selected;</script><text>Highlight NES Region (237-327)</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; select 576-648; color magenta; wireframe off; spacefill off; zoom 200; center selected;</script><text>Highlight NLS Region (576-648)</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; wireframe off; select protein; trace only; select 288,304; spacefill 120; color yellow; center selected; zoom 300;</script><text>Show NES Phosphorylation Sites</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; wireframe off; select protein; trace only; select 582,620,625,633; spacefill 120; color yellow; center selected; zoom 300;</script><text>Show NLS Phosphorylation Sites</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; select 647-698; color purple; wireframe off; spacefill off; select ZN; spacefill 120; color cpk; zoom 350; center selected;</script><text>DNA Binding Domain with Zinc</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; set cartoonFancy true; cartoon; color structure; select helix; color red; select sheet; color yellow; select turn; color green; select ZN; spacefill; color cpk; zoom 150;</script><text>Show Secondary Structure</text></jmolButton></jmol>
 +
<jmol><jmolButton><script>select all; cartoon; color chain; wireframe off; spacefill off; labels off; spin off; zoom 100; center all;</script><text>Reset View</text></jmolButton></jmol>
-
=== Interactive Molecular Tour ===
 
-
Explore Msn2’s structural features using the buttons below, powered by JSmol scripts adapted from the [JSmol documentation](https://chemapps.stolaf.edu/jmol/docs/):
+
<jmol>
 +
<jmolButton>
 +
<script>
 +
select 640-704; cartoon; color bfactor;
 +
spacefill 0.5; color cpk;
 +
</script>
 +
<text>Putative Zn-Coordinating Cys/His</text>
 +
</jmolButton>
 +
</jmol>
<jmol>
<jmol>
-
<jmolButton>
+
<jmolButton>
-
<script>select all; cartoon on; color structure; spacefill off;</script>
+
<script>
-
<text>Show Cartoon View</text>
+
select 570-650; cartoon; color magenta;
-
</jmolButton>
+
select 582,620,625,633; spacefill off;
-
<jmolButton>
+
select 576-648 and (lys or arg); spacefill 0.7; color blue;
-
<script>select 649-670; color red; select 649 and atomName=CA; label "Zinc Finger 1"; select 676-698; color blue; select 676 and atomName=CA; label "Zinc Finger 2";</script>
+
</script>
-
<text>Highlight Zinc Fingers</text>
+
<text>Basic Residues in NLS</text>
-
</jmolButton>
+
</jmolButton>
-
<jmolButton>
+
-
<script>select 288; spacefill on; color yellow; select 288 and atomName=CA; label "S288"; select 582; spacefill on; color yellow; select 582 and atomName=CA; label "S582"; select 620; spacefill on; color yellow; select 620 and atomName=CA; label "S620"; select 625; spacefill on; color yellow; select 625 and atomName=CA; label "S625"; select 633; spacefill on; color yellow; select 633 and atomName=CA; label "S633"; select 686; spacefill on; color yellow; select 686 and atomName=CA; label "S686";</script>
+
-
<text>Show PKA Phosphorylation Sites</text>
+
-
</jmolButton>
+
-
<jmolButton>
+
-
<script>select all; spacefill on; color cpk; cartoon off;</script>
+
-
<text>Show Spacefill View</text>
+
-
</jmolButton>
+
-
<jmolButton>
+
-
<script>select all; backbone 0.5; color chain; cartoon off; spacefill off;</script>
+
-
<text>Show Backbone Trace</text>
+
-
</jmolButton>
+
-
<jmolButton>
+
-
<script>reset; labels off; select all; cartoon on; color structure; spacefill off;</script>
+
-
<text>Reset View</text>
+
-
</jmolButton>
+
</jmol>
</jmol>
-
=== Zinc Finger Domains ===
+
incorporate
-
Msn2 has two C2H2 zinc finger domains at residues 649–670 and 676–698, critical for binding STREs (5'-CCCCT-3') in DNA ([SGD: MSN2](https://www.yeastgenome.org/locus/S000004640)). These domains, identified in the sequence (NP_013751.1), coordinate zinc ions via cysteine and histidine residues, stabilizing the DNA-binding motif.
+
https://proteopedia.org/wiki/index.php/User:Jaime_Prilusky/JSmolExtension/Tags_for_In-page_Models
-
=== Phosphorylation Sites ===
+
https://chemapps.stolaf.edu/jmol/docs/
-
Msn2 is phosphorylated on 22 residues, with six key sites regulated by PKA: S288, S582, S620, S625, S633, and S686. These sites, particularly within the nuclear localization signal (NLS), control Msn2’s shuttling between cytoplasm and nucleus, impacting its transcriptional activity ([Gallmetzer et al., 2018](https://www.molbiolcell.org/doi/10.1091/mbc.E18-06-0389)).
+
<jmol><jmolButton><script>select all; cartoon; color structure; spacefill off; labels off;</script><text>Show Overall Structure</text></jmolButton></jmol>
-
=== AlphaFold Model ===
+
<jmol><jmolButton><script>select all; cartoon; color structure; select 647-665; color red;</script><text>Highlight Zinc Finger 1 (647-665)</text></jmolButton></jmol>
-
The structure is an AlphaFold-predicted model, offering a reliable depiction of Msn2’s 704-amino-acid structure. AlphaFold’s deep learning approach predicts the protein’s fold, including the zinc finger domains and regions containing phosphorylation sites, based on the sequence from [UniProt: P33748](https://www.uniprot.org/uniprotkb/P33748/entry).
+
<jmol><jmolButton><script>select all; cartoon; color structure; select 676-698; color blue;</script><text>Highlight Zinc Finger 2 (676-698)</text></jmolButton></jmol>
-
== References ==
+
<jmol><jmolButton><script>select all; cartoon; color structure; select 237-327; color green;</script><text>Highlight NES Region (237-327)</text></jmolButton></jmol>
-
* [UniProt: P33748 (MSN2_YEAST)](https://www.uniprot.org/uniprotkb/P33748/entry)
+
<jmol><jmolButton><script>select all; cartoon; color structure; select 576-648; color magenta;</script><text>Highlight NLS Region (576-648)</text></jmolButton></jmol>
-
* [SGD: MSN2 Locus Summary](https://www.yeastgenome.org/locus/S000004640)
+
 
-
* [Msn2 Coordinates a Stoichiometric Gene Expression Program](https://www.sciencedirect.com/science/article/pii/S0960982213011901)
+
<jmol><jmolButton><script>select all; cartoon; color structure; spacefill off; select 288,304; spacefill; color yellow;</script><text>Highlight NES Phosphorylation Sites (S288, S304)</text></jmolButton></jmol>
-
* [Constitutive Active Allele of Msn2 Mimicking Low PKA Activity](https://www.molbiolcell.org/doi/10.1091/mbc.E18-06-0389)
+
 
-
* [JSmol Interactive Scripting Documentation](https://chemapps.stolaf.edu/jmol/docs/)
+
<jmol><jmolButton><script>select all; cartoon; color structure; spacefill off; select 582,620,625,633; spacefill; color yellow;</script><text>Highlight NLS Phosphorylation Sites (S582, S620, S625, S633)</text></jmolButton></jmol>
 +
 
 +
<jmol><jmolButton><script>select all; cartoon; color structure; spacefill off; select 686; spacefill; color yellow;</script><text>Highlight DBD-proximal Phosphorylation Site (S686)</text></jmolButton></jmol>
 +
 
 +
<jmol><jmolButton><script>select all; cartoon; color structure; spacefill off; labels off;</script><text>Reset View</text></jmolButton></jmol>
 +
 
 +
</StructureSection>

Current revision

Your Heading Here (maybe something like 'Structure')

Caption for this structure

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Joseph M. Steinberger

Retrieved from "http://52.214.119.220/wiki/index.php/JMS/Sandbox/msn2_1"
Personal tools