JMS/Sandbox/msn2 1

<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).

=== 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 all; cartoon on; color structure; spacefill off;</script>

<text>Show Cartoon View</text>

</jmolButton>

<jmolButton>

<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>

<text>Highlight Zinc Fingers</text>

</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>

=== Zinc Finger Domains ===

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.

=== Phosphorylation Sites ===

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)).

=== AlphaFold Model ===

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).

== References ==

* [UniProt: P33748 (MSN2_YEAST)](https://www.uniprot.org/uniprotkb/P33748/entry)

* [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)

* [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/)