Journal:Acta Cryst D:S2059798322002157
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| - | <StructureSection load='' size='450' side='right' scene=' | + | <StructureSection load='' size='450' side='right' scene='90/905553/Cv/2' caption=''> |
| - | ===The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models : a case study report | + | ===The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case study report=== |
| - | <big>Irène Barbarin- | + | <big>Irène Barbarin-Bocahu, Marc Graille</big> <ref>doi: 10.1107/S2059798322002157</ref> |
<hr/> | <hr/> | ||
<b>Molecular Tour</b><br> | <b>Molecular Tour</b><br> | ||
| + | Depending on their amino acid sequences, the proteins fold into specific three-dimensional (3D) structures, which are crucial to fulfill their cellular and biochemical functions. The knowledge of the 3D structure of all the proteins is then very important to appreciate their biological and biochemical functions as well as the potential impact of mutations associated with diseases. Very high accuracy in protein 3D structure prediction has recently been reached by the deep-learning based programs AlphaFold or RoseTTAFold. | ||
| + | Here, we take advantage of these high quality models to solve the crystal structure of a yeast protein involved in an mRNA quality control pathway. This article illustrates one of the important applications of 3D protein structure models generated by AlphaFold or RoseTTAFold programs, i.e. in solving the X-ray crystallography phase problem. We discuss the different strategies to generate search models. Finally, this article also contributes to the validation of the very high quality of these models. | ||
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| + | The ''Kl''Nmd4 protein is made of a three layered 𝛼/β/𝛼 core consisting in a central five stranded parallel β-sheet surrounded by six 𝛼-helices (𝛼1 to 𝛼4, 𝛼10 and 𝛼11) on one side and five (𝛼5 to 𝛼9) on the other side. <scene name='90/905553/Cv/4'>Ribbon representation of the KlNmd4 crystal structure</scene> colored from its N-terminal (blue) to its C-terminal (red) extremities. | ||
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| + | <scene name='90/905553/Cv/8'>Superposition of the full-length KlNmd4 AlphaFold model onto the KlNmd4 crystal structure</scene> (beige). The full-length KlNmd4 AlphaFold model is colored according to the pLDDT values: | ||
| + | *pLDDT > 90 <span class="text-blue">'''blue'''</span> | ||
| + | *70 < pLDDT < 90 <span class="bg-lightcyan">cyan</span> | ||
| + | *50 < pLDDT < 70 <span class="bg-yellow">yellow</span> | ||
| + | *pLDDT < 50 <span class="bg-orange">orange</span> | ||
| + | The region 81-114 from the KlNmd4 crystal structure is highlighted in <span class="bg-pink">pink</span>. | ||
| + | |||
| + | Morph representing superposition of the full-length KlNmd4 AlphaFold model onto the KlNmd4 crystal structure: | ||
| + | *1) <scene name='90/905553/Cv/9'>KlNmd4 crystal structure</scene> in <span class="bg-lightgreen">green</span>. | ||
| + | *2) <scene name='90/905553/Cv/10'>KlNmd4 AlphaFold model</scene> in <span class="text-red">'''red'''</span>. | ||
| + | *3) <scene name='90/905553/Cv/11'>Superposition of the full-length KlNmd4 AlphaFold model onto the KlNmd4 crystal structure</scene>. | ||
| + | <jmol><jmolButton> | ||
| + | <script>if (_animating); anim pause;set echo bottom left; color echo white; font echo 20 sansserif;echo Animation Paused; else; anim resume; set echo off;endif;</script> | ||
| + | <text>Click here to Stop Animation before next scene.</text> | ||
| + | </jmolButton></jmol> | ||
| + | *4) <scene name='90/905553/Cv/12'>This scene without animation</scene>. | ||
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| + | '''PDB reference:''' ''Kluyveromyces lactis'' Nmd4, [[7qhy]]. | ||
<b>References</b><br> | <b>References</b><br> | ||
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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.
