EOM homotetramer - alignment problems error

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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EOM homotetramer - alignment problems error

#1 Post by ctome » 2018.01.31 16:11


I am working with a two-domain protein. Domain 2 assembles to form a homotetramer (I have a PDB structure of the tetrameric D2). Domain 1 is connected by a flexible linker and can adopt different positions (there is a PDB structure of D1 alone). I am trying to use EOM to describe preferential positions of domains 1 in the tetramer, while maintaining the interface between domains 2 intact.

I built a model of the entire tetramer based on the conformation of similar proteins.
I ran alpraxin on this model, and from the *r.pdb I built five files: one tetramerD2.pdb, and four D1.pdb files.
I used these five domains as input to EOM, and said that tetramerD2.pdb contains multiple chains.
EOM gives this error message: Alignment Problems: check the sequence and the domains.
For the .seq file, I tried using both my construct sequence (full-length and tagged monomeric protein), and the sequence extracted with pdb2seq from the model (as the PDB structure is missing some residues).

Could you help me with what might be wrong with the seq/pdb files that I am providing?
Should I be using a different protocol for running EOM?

Thank you,

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Re: EOM homotetramer - alignment problems error

#2 Post by mawhite » 2018.02.02 00:41


You need to put the four D2 domains into separate files and then fix their position in EOM. The protein.seq file needs just one chain, and any linkers. Linkers should be at least 4 aa long..

echo "AAAA" > protein.seq
pdb2seq D1_A.pdb >> protein.seq
echo "AAAAAA" >> protein.seq
pdb2seq D2_A.pdb >> protein.seq
echo "AAHHHHHH" >> protein.seq

It is best to move all the models to the origin, and correctly spaced to each other, before running EOM with a fixed domain.

Good luck,

PS. If you align the tetramer D2 4-fold axis along Z you can run EOM with P4 symmetry and only one chain.

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