Journal:MicroPubl Biol:000574
From Proteopedia
(Difference between revisions)
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*Very high (pLDDT > 90) <span class="text-blue">'''blue'''</span> | *Very high (pLDDT > 90) <span class="text-blue">'''blue'''</span> | ||
| - | The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. <scene name='91/919077/Cv/5'>A structural overlay</scene> of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB [[6j9c]]), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated <scene name='91/919077/Cv/6'>positively charged residues surrounding the DNA-binding site</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) that could interact with the negatively charged DNA backbone and mapping of the level of conservation for each residue showed that <scene name='91/919077/Cv/10'>the residues within this site were all highly conserved</scene> among homologs of this protein, as determined by the ConSurf program. | + | The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. <scene name='91/919077/Cv/5'>A structural overlay</scene> of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB [[6j9c]]), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated <scene name='91/919077/Cv/6'>positively charged residues surrounding the DNA-binding site</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) that could interact with the negatively charged DNA backbone and mapping of the level of conservation for each residue showed that <scene name='91/919077/Cv/10'>the residues within this site were all highly conserved</scene> among homologs of this protein, as determined by the ConSurf program. [[Image:Consurf_key_small.gif|left|thumb]] |
<b>References</b><br> | <b>References</b><br> | ||
Revision as of 11:39, 11 August 2022
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This page complements a publication in scientific journals and is one of the Proteopedia's Interactive 3D Complement pages. For aditional details please see I3DC.
