I'm sort of new to visualization of crystal structure so please bear with me. I'm working with Chimera as my viewer as of the moment.
I'm wondering how the following extended conformation of the integrin below was generated and if it can be done through Chimera. As far as I know, the bent crystal structure is available (PDB 1JV2). The study though (Article Crystal Structure of the Extracellular Segment of Integrin a...
) indicated how the rotation was done. I've been trying to tweak certain components but I can't still figure out how to do it.I'm also wondering how they connected the transmembrane and cytoplasmic regions of the integrin. The figure caption stated that "have been pasted at the bottom of the extracellular domains." I'm not sure what "pasted" meant, if it's just added like graphically or generated by combining the sequences. I'm trying to decipher this as I also want to work on generating chimeric structures with linkers.
Using Blast protein option in Chimera, knowing the probable residue sequence one can generate the structure. You can append the sequence of any linker or extended part to the protein.
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