JMS/Sandbox/msn2
From Proteopedia
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| - | {{DISPLAYTITLE:MSN2 (P33748) — Stress-responsive transcription factor}} | ||
| - | __NOTOC__ | ||
| - | == Interactive 3-D Model == | ||
<Structure load='AF-P33748-F1-model v4.pdb' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /> | <Structure load='AF-P33748-F1-model v4.pdb' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /> | ||
| - | <applet load='AF-P33748-F1-model_v4.pdb' size='400' align='right' caption='AlphaFold model of MSN2 (P33748)'> | ||
| - | <jmolLink> | ||
| - | <script> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; # AlphaFold prediction :contentReference[oaicite:0]{index=0}:contentReference[oaicite:1]{index=1} | ||
| - | select protein; cartoon on; color chain; wireframe off; spacefill off; | ||
| - | zoom 1.3; | ||
| - | </script> | ||
| - | <text>Initial full-length model</text> | ||
| - | </jmolLink> | ||
| - | </applet> | ||
| - | |||
| - | * [[Full-length model]] (restore the starting view) | ||
| - | * [[Zinc finger DNA-binding domain]] | ||
| - | * [[Regulated nuclear-localization signal (NLS)]] | ||
| - | * [[PKA phosphorylation cluster]] | ||
| - | * [[C2H2 zinc-binding motif]] | ||
| - | * [[Intrinsically disordered regions (IDRs)]] | ||
| - | * [[Confidence coloring (pLDDT)]] | ||
| - | |||
| - | ---- | ||
| - | <scene name='Full-length model'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select protein; cartoon on; color chain; wireframe off; spacefill off; | ||
| - | zoom 1.3; | ||
| - | </scene> | ||
| - | |||
| - | <scene name='Zinc finger DNA-binding domain'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select 645-704; center selected; zoom 2.4; | ||
| - | cartoon on; color structure; wireframe off; spacefill off; | ||
| - | select 678,681,694,698; spacefill 0.45; color CPK; # Zn-coordinating Cys/His | ||
| - | </scene> | ||
| - | |||
| - | <scene name='Regulated nuclear-localization signal (NLS)'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select 618-633; center selected; zoom 2.5; | ||
| - | cartoon on; color yellow; wireframe off; spacefill off; | ||
| - | select 618-633 and (LYS,ARG); spacefill 0.5; color hotpink; # basic residues | ||
| - | </scene> | ||
| - | |||
| - | <scene name='PKA phosphorylation cluster'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select protein; cartoon on; color structure; wireframe off; spacefill off; | ||
| - | select 582,620,625,633; center selected; zoom 2.5; | ||
| - | spacefill 0.7; color yellow; # key PKA sites | ||
| - | </scene> | ||
| - | |||
| - | <scene name='C2H2 zinc-binding motif'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select 678,681,694,698; center selected; zoom 3.0; | ||
| - | cartoon on; color gray; wireframe off; spacefill off; | ||
| - | spacefill 0.6; color hotpink; | ||
| - | </scene> | ||
| - | |||
| - | <scene name='Intrinsically disordered regions (IDRs)'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select 1-600; cartoon on; color cyan; | ||
| - | select 645-704; cartoon on; color salmon; | ||
| - | wireframe off; spacefill off; zoom 1.3; | ||
| - | </scene> | ||
| - | |||
| - | <scene name='Confidence coloring (pLDDT)'> | ||
| - | load $DATA/AF-P33748-F1-model_v4.pdb; | ||
| - | select protein; cartoon on; wireframe off; spacefill off; | ||
| - | color bfactor; # AlphaFold stores pLDDT in B-factor field | ||
| - | zoom 1.3; | ||
| - | </scene> | ||
| - | |||
| - | ---- | ||
| - | == Quick Guide == | ||
| - | * **C-terminal zinc finger (645-704)** binds STRE/G-quadruplex DNA. | ||
| - | * **Regulated NLS (618-633)** is masked by **PKA phosphorylation** (S582, S620, S625, S633) to control stress-dependent nuclear import. | ||
| - | * Most of the N-terminal 600 aa are **intrinsically disordered**, housing the NES and trans-activation motifs. | ||
| - | * Per-residue **pLDDT** values (confidence coloring scene) highlight the single well-folded domain vs. the flexible IDRs. | ||
| - | |||
| - | AlphaFold PDB header and full sequence: :contentReference[oaicite:2]{index=2}:contentReference[oaicite:3]{index=3} | ||
Revision as of 14:32, 4 May 2025
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