JMS/Sandbox/msn2 1
From Proteopedia
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* [Constitutive Active Allele of Msn2 Mimicking Low PKA Activity](https://www.molbiolcell.org/doi/10.1091/mbc.E18-06-0389) | * [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/) | * [JSmol Interactive Scripting Documentation](https://chemapps.stolaf.edu/jmol/docs/) | ||
| - | |||
| - | Below is an example of a **Proteopedia page** for Msn2 from budding yeast (*Saccharomyces cerevisiae*) that you can **copy-paste** in its entirety. It uses **inline JSmol scripting** to highlight features such as the DNA-binding Zn-finger domain, disordered regions, phosphorylation sites, and nuclear localization signals (NLS). The Jmol commands are adapted from [Jmol’s documentation](https://chemapps.stolaf.edu/jmol/docs/). Adjust scene names, residue ranges, and color schemes as desired. | ||
| - | |||
| - | --- | ||
| - | |||
| - | ``` | ||
| - | {{Protein Data Bank Header | ||
| - | |title=Msn2 from Saccharomyces cerevisiae (AlphaFold model) | ||
| - | |classification=Transcription Factor | ||
| - | }} | ||
| - | |||
| - | == Introduction == | ||
| - | ''Msn2'' is a key stress-responsive transcription factor in budding yeast (*Saccharomyces cerevisiae*). Under stress conditions (e.g., low glucose, heat shock, oxidative stress), Msn2 rapidly translocates to the nucleus, where it binds specific DNA elements (STREs) and activates genes important for survival. This page explores the AlphaFold-predicted model of Msn2, highlighting its main structured region (a zinc-finger DNA-binding domain) and multiple intrinsically disordered segments that regulate its activity via phosphorylation, nuclear localization signals, and interactions with cofactors. | ||
| - | |||
| - | == Overview of the AlphaFold Structure == | ||
| - | |||
| - | <StructureSection size='340' side='right' caption='AlphaFold Model of Msn2' scene='Msn2_mainScene'> | ||
| - | <scene name='Msn2_mainScene' script=" | ||
| - | # Load and basic display setup | ||
| - | select all | ||
| - | cartoons on | ||
| - | wireframe off | ||
| - | spacefill off | ||
| - | color structure | ||
| - | |||
| - | # Optional background color | ||
| - | background white | ||
| - | |||
| - | # Spin the molecule for an interactive look | ||
| - | spin on | ||
| - | |||
| - | # Center and zoom to show the overall structure | ||
| - | center all | ||
| - | zoom 140 | ||
| - | "> | ||
| - | This main scene shows the overall predicted structure of Msn2 based on AlphaFold. | ||
| - | </scene> | ||
| - | </StructureSection> | ||
| - | |||
| - | Msn2 is predominantly disordered throughout its N-terminal half, encompassing the so-called transcriptional activation domain, which interacts with cofactors. However, the C-terminal half contains two C2H2 zinc fingers (residues ~624–704) that bind DNA. Multiple phosphorylation sites modulate its nucleocytoplasmic localization and transcriptional activity, including key sites near the nuclear localization signals (NLS). | ||
| - | |||
| - | == Highlighting the DNA-Binding Zn-Finger Domain == | ||
| - | |||
| - | <scene name='Msn2_ZnFinger' script=" | ||
| - | # Turn on cartoon, color it uniformly for context | ||
| - | select all | ||
| - | cartoons on | ||
| - | color grey | ||
| - | |||
| - | # Highlight the Zn-finger domain (e.g., ~624-704) in orange | ||
| - | select 624-704 | ||
| - | color orange | ||
| - | |||
| - | # Center on the middle of the Zn-fingers and zoom in | ||
| - | center 660 | ||
| - | zoom 200 | ||
| - | |||
| - | # Optionally label the domain | ||
| - | label /1:660 'Zn-Finger Domain' | ||
| - | "> | ||
| - | Here we highlight the zinc-finger domain (residues ~624–704), which is essential for DNA binding. | ||
| - | </scene> | ||
| - | |||
| - | These two C2H2 zinc fingers recognize STRE (stress response element) sequences in promoters of stress-related genes. | ||
| - | |||
| - | == Visualizing Intrinsically Disordered Regions == | ||
| - | |||
| - | <scene name='Msn2_Disorder' script=" | ||
| - | # Show entire protein in a thin trace | ||
| - | select all | ||
| - | wireframe 100 | ||
| - | spacefill off | ||
| - | cartoons off | ||
| - | color grey | ||
| - | |||
| - | # Now show the structured Zn-finger portion in a cartoon, for contrast | ||
| - | select 624-704 | ||
| - | wireframe off | ||
| - | cartoons on | ||
| - | color cyan | ||
| - | |||
| - | # Provide a textual label illustrating the boundary | ||
| - | label /1:650 'N-term (mostly disordered)' | ||
| - | label /1:680 'C-term Zn-Finger' | ||
| - | zoom 140 | ||
| - | "> | ||
| - | Most of the N-terminal half of Msn2 is predicted to be disordered and flexible, while the C-terminal Zn-finger domain adopts a well-defined fold. | ||
| - | </scene> | ||
| - | |||
| - | Many phosphorylation sites lie within this disordered N-terminus, providing rapid and dynamic control of Msn2’s function. | ||
| - | |||
| - | == Phosphorylation Sites (PKA Target Serines) == | ||
| - | |||
| - | <scene name='Msn2_Phosphosites' script=" | ||
| - | # Start with a cartoon view | ||
| - | select all | ||
| - | cartoons on | ||
| - | color white | ||
| - | spacefill off | ||
| - | |||
| - | # Highlight key serines known to be phosphorylated (e.g., near NLS) | ||
| - | # For demonstration, we list typical PKA sites: S582, S620, S625, S633, S638 | ||
| - | select 582,620,625,633,638 | ||
| - | spacefill 200 | ||
| - | color red | ||
| - | |||
| - | # Label each site | ||
| - | label /1:582 'S582' | ||
| - | label /1:620 'S620' | ||
| - | label /1:625 'S625' | ||
| - | label /1:633 'S633' | ||
| - | label /1:638 'S638' | ||
| - | |||
| - | # Center on the region around residue 620 | ||
| - | center 620 | ||
| - | zoom 200 | ||
| - | "> | ||
| - | Several serines in the vicinity of the nuclear localization signals are phosphorylated by PKA. Under non-stress conditions, these phosphorylations contribute to cytoplasmic retention of Msn2. | ||
| - | </scene> | ||
| - | |||
| - | Dephosphorylation of these sites during stress permits nuclear entry and gene activation. | ||
| - | |||
| - | == Nuclear Localization Signals (NLS) == | ||
| - | |||
| - | <scene name='Msn2_NLS' script=" | ||
| - | # C-terminal region in cartoon | ||
| - | select all | ||
| - | cartoons on | ||
| - | color grey | ||
| - | |||
| - | # Color the NLS clusters in green (e.g., around 573–590 and 620–639) | ||
| - | select 573-590 or 620-639 | ||
| - | color green | ||
| - | |||
| - | # Center and zoom to show the NLS near the Zn-finger domain | ||
| - | center 600 | ||
| - | zoom 180 | ||
| - | |||
| - | # Optional: turn on spin for a dynamic look | ||
| - | spin on | ||
| - | "> | ||
| - | Two NLS segments in Msn2 are highlighted in green. Their phosphorylation state determines nuclear import efficiency. | ||
| - | </scene> | ||
| - | |||
| - | == Measuring Zn-Finger Coordination (Example of a Distance Measure) == | ||
| - | |||
| - | <scene name='Msn2_DistanceMeasure' script=" | ||
| - | # Turn off any previous measures | ||
| - | measure delete * | ||
| - | |||
| - | # Show cartoon for context | ||
| - | select all | ||
| - | cartoons on | ||
| - | color grey | ||
| - | |||
| - | # Identify (example) two Zn-coordinating residues in the first Zn finger | ||
| - | # Let's say these are Cys626 and His630 (fictitious example positions) | ||
| - | select 626, 630 | ||
| - | spacefill 200 | ||
| - | color yellow | ||
| - | label /1:626 'Cys626' | ||
| - | label /1:630 'His630' | ||
| - | |||
| - | # Measure the distance | ||
| - | measure distance {1:626} {1:630} | ||
| - | color measures black | ||
| - | |||
| - | # Center on Zn-finger and zoom | ||
| - | center 628 | ||
| - | zoom 250 | ||
| - | "> | ||
| - | This scene measures the distance between two putative zinc-coordinating residues (Cys626 and His630). Jmol’s ''measure distance'' command is useful to confirm geometry around metal-binding sites. | ||
| - | </scene> | ||
| - | |||
| - | == Nuclear Export Signal (NES) Region == | ||
| - | |||
| - | <scene name='Msn2_NES' script=" | ||
| - | # Show cartoon for the entire protein | ||
| - | select all | ||
| - | cartoons on | ||
| - | color grey | ||
| - | |||
| - | # Emphasize the NES region (e.g., ~270–300) | ||
| - | select 270-300 | ||
| - | cartoons off | ||
| - | wireframe 150 | ||
| - | color magenta | ||
| - | |||
| - | # Provide labels | ||
| - | label /1:288 'Ser288' | ||
| - | center 288 | ||
| - | zoom 200 | ||
| - | "> | ||
| - | A leucine-rich NES around residues 270–300, including Ser288, regulates nuclear export of Msn2. Phosphorylation here also modulates cytoplasmic retention. | ||
| - | </scene> | ||
| - | |||
| - | == Additional Notes == | ||
| - | * The above scenes illustrate different regulatory features of Msn2. | ||
| - | * Residue numbering may vary in different Msn2 isoforms or structural models. | ||
| - | * For real structural validation, consider comparing with experimental data if available. | ||
| - | |||
| - | == References == | ||
| - | * Görner, W., et al. (2002). ''Nuclear localization of the C2H2 zinc finger protein Msn2 is regulated by stress and protein kinase A activity in yeast.'' EMBO J. **21**(1):135–144. | ||
| - | * Gasch, A.P., et al. (2000). ''Genomic expression programs in the response of yeast cells to environmental changes.'' Mol. Biol. Cell. **11**(12):4241–4257. | ||
| - | * De Wever, V., et al. (2005). ''Phosphorylation of serine 288 in the nuclear export signal of Msn2 by protein kinase A modulates Msn2 nuclear localization.'' J. Biol. Chem. **280**(46):37193–37198. | ||
| - | * AlphaFold Protein Structure Database: [Msn2 (P13382)](https://alphafold.ebi.ac.uk/entry/P13382) | ||
| - | |||
| - | ---- | ||
| - | |||
| - | ''Copy and paste the entire text above into a Proteopedia page and adjust the scene names, residue ranges, or color schemes to suit your needs. Each <scene> tag includes an inline JSmol script adapted from [Jmol’s documentation](https://chemapps.stolaf.edu/jmol/docs/). Feel free to tweak them further for your final Msn2 article!'' | ||
| - | |||
| - | --- | ||
| - | |||
| - | **Note**: In Proteopedia, you can embed additional descriptive text or images around these `<scene>` tags. If needed, replace the numeric ranges or residue numbers based on your alignment of Msn2. You may also change the coloring or labeling schemes. This template simply provides a comprehensive starting point for your Msn2 molecular tour! | ||
| - | ``` | ||
Revision as of 13:28, 11 May 2025
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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).
Contents |
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/):
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/)
