Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
DOI10.5281/zenodo.3951861Zenodo3951861MaRDI QIDQ6709804FDOQ6709804
Dataset published at Zenodo repository.
Jeremy Copperman, Kimberly Dolan, Janette Myers, Craig Yoshioka, Jonathan Flores, Bassam Haddad, Daniel M. Zuckerman, Steve Reichow
Publication date: 28 August 2020
Copyright license: Creative Commons Attribution 4.0 International
These are the molecular dynamics (MD) data that are analyzed, in Flores et al. 2020. Each trajectory file (.dcd) has an associated structure file (.psf), which can be analyzed in VMD. Each gap junction system, Cx46 Cx50, were simulated with either KCl or NaCl in the intracellular space: Cx46_KCl/NaCl, Cx50_KCl/NaCl. All four systems were equilibrated for 30ns and then followed up with 2 separate 100ns production runs. For MD lipid-densities the Cx50_KCl system was used as the representative dataset. Lipid densities from all other systems can be calculated with the provided TCL script calc-density.tcl. In VMD TK-Console: mol new system.psf mol addfile system.dcd waitfor all source /path/to/scripts/LipNetwork.tcl align source /path/to/scripts/calc-density.tcl dmpcdensity outname [output] outname_ltailden.dx Convert from .dx to .mrc using UCSF-ChimeraVolume_Viewerplugin. [output] outname_ltailden.mrc Using Relion: $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6 [output]outname_ltailden_D6-Sym.mrc All trajectory files (.dcd) are 100ns longs (1,000 frames x 100ps/frame). For questions regarding MD-data analysis andfull trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).
This page was built for dataset: Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
