AlphaFold2 examples from CASP 14: Difference between revisions
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==Phage RNA polymerase== | ==Phage RNA polymerase== | ||
Our second example is a 404-residue domain within a 2,180 residue RNA polymerase, [[6vr4]], gp66 from a bacteriophage of the crAss-like group, some members of which are prevalent in the human gut<ref name="T1037" />. One known host for the target-containing phage is gram-negative, aerobic bacteria ''Cellulphaga baltica'' isolated from marine | Our second example is a 404-residue domain within a 2,180 residue RNA polymerase, [[6vr4]], gp66 from a bacteriophage of the crAss-like group, some members of which are prevalent in the human gut<ref name="T1037" />. One known host for the target-containing phage is gram-negative, aerobic bacteria ''Cellulphaga baltica'' isolated from marine microalgae<ref name="cb">PMID: 10425785</ref>. CASP 14 classified this domain, coded T1037, as a free modeling ("FM") target, meaning that no informative templates existed in the [[PDB]]. | ||
===X-ray crystal structure=== | ===X-ray crystal structure=== | ||
The crystallographic structure, not available to the prediction teams during the CASP competition, is [[6vr4]], with [[resolution]] 3.5 Å, and an Rfree "reliability" of "much better than average for this resolution" (according to [[FirstGlance in Jmol]]). The termini of the chain are far apart from each other (~85 Å), and there are no disulfide bonds. | The crystallographic structure, not available to the prediction teams during the CASP competition, is [[6vr4]], with [[resolution]] 3.5 Å, and an Rfree "reliability" of "much better than average for this resolution" (according to [[FirstGlance in Jmol]]). The termini of the chain are far apart from each other (~85 Å), and there are no disulfide bonds. | ||
The CASP 14 target sequence of 404 residues begins at sequence number 337 and ends at 901, a span of 565 residues. The target sequence is 404 residues because it excludes residues 370-530 (length 161), which form a different domain. <scene name='87/875686/6vr4_b_2180_residues/4'>Here is the full 2,180 residue chain with 337-901 (565 residues) opaque</scene>. Here is <span style="color:#d000d0;"><b>the 404-residue target sequence </b></span> with the <span class="text-gray"><b>intervening domain | The CASP 14 target sequence of 404 residues begins at sequence number 337 and ends at 901, a span of 565 residues. The target sequence is 404 residues because it excludes residues 370-530 (length 161), which form a different domain. <scene name='87/875686/6vr4_b_2180_residues/4'>Here is the full 2,180 residue chain with 337-901 (565 residues) opaque</scene>. Here is <span style="color:#d000d0;"><b>the 404-residue target sequence </b></span> with the <span class="text-gray"><b>intervening domain (excluded from the CASP target)</b> <scene name='87/875686/6vr4_b_2180_residues/5'>highlighted within the full 2,180-residue chain</scene>. | ||
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