Cryo-EM maps of 48 nm-repeating structures of doublets from wildtype mouse, Tekt5 -/- mouse and human sperm have been deposited in the Electron Microscopy Data Bank (EMDB) with accession codes: EMD-41431, EMD-41320 and EMD-41317, respectively. The EMD-41431 is a composite map with its two submaps deposited with accession codes: EMD-41450 and EMD-41451. Maps of focused refinement of 16 nm-repeating structures of A- and B-tubules from wildtype mouse have been deposited also: EMD-41315 and EMD-41316. The atomic model of the 48-nm repeat of the mouse sperm doublets has been deposited in the Protein Data Bank (PDB) with accession codes 8TO0. MS data are shared and available through the ProteomeXchange Consortium via the PRIDE partner repository under the dataset identifier: PXD036885 (username: reviewer_pxd036885@ebi.ac.uk; password: tMEZ90MC).56 R package source materials for MSstats (version 3) are publicly available through the Krogan Lab GitHub: https://github.com/kroganlab.
After downloading the AlphaFold2 library of the mouse proteome, this code is used to distribute PDB files into subdirectories.�=0;
for f in ∗;
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do
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## Splitting 50 PDBs in each subdirectory
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d=dir_$(printf %03d $((i/50+1)));
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mkdir -p $d;
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mv "$f" $d;
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let i++;
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done
This code is used to unbiasedly match all PDBs with the target densities in each subdirectory:
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for file in ∗
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do
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echo $file
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## CCDC105_flipped_b150.mrc is the target densities, the options could be found in the situs website
colores ../CCDC105_flipped_b150.mrc ${file} -res 6.0 -cutoff 0.0048 -deg 15.0 mkdir../output/${file}_out
mv col_∗../output/${file}_out/.
mv
done
The cross-correlation scores could then be extracted using the following script:
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for f in ∗_outt
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do
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echo $f
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grep structure $f/∗.pdb >> TheResultFile
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grep Unnormalized $f/∗.pdb >> TheResultFile
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done
grep "correlation" TheResultFile > JustCCResults
The final output could then be sorted based on the cross-correlation scores in Excel. Note each PDB would be matched to the target densities with multiple orientations, resulting in multiple entries with the same PDB but different cross-correlation scores. The duplicate items for each PDB could be deleted in Excel.
Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request.