MD package of wtXPD-damaged-ssDNA
Year: 2023
Type: dataset
Abstract: MD simulation: wtXPD-damaged-ssDNAXPD-64PP.tgz and XPD-CPD.tgz The 8 µs MD simulations of human XPD bound to damaged ssDNA, containing a 6−4PP (XPD-64PP) or a CPD (XPD-CPD) lesion right outside the entry pore of XPD, are provided. Descriptions of each simulations 1. Simulation of XPD-64PP reveals that 6−4PP initially positioned outside the entry pore is translocated in the 3' to 5' direction as its bases flip into the unoccupied space within the pore. 2. Simulation of XPD-CPD reveals that CPD initially positioned outside the DNA entry pore undergoes a backbone-translocation into the pore, but its bases are blocked from entering. Files included For each system, the trajectory files are presented in binary NETCDF format, *.nc, a corresponding topology PRMTOP files, *.top, and the coordinates of the initial structure in PDB files, *.pdb are also provided, where * = XPD-64PP, XPD-CPD. Note 1. Water molecules and ions are not included in all files. 2. The trajectories were saved every 1 ns.Coordinates of the model of XPG-XPD-XPB bound to the open bubble substrate XPG-XPD-XPB-initial.pdb and XPG-XPD-XPB-final.pdbXPG-XPD-XPB-initial.pdb: XPD prior to the shift of the Arch domain within the XPG-XPD-XPB-DNA complex. XPG-XPD-XPB-final.pdb: XPD after the shift of the Arch domain within the XPG-XPD-XPB-DNA complex.Note This model is derived from the structural model provided by Bralic et al. In this model, XPB and XPD helicase were replaced with those in the exiting cryo-EM structure of TFIIH-XPA-DNA; XPG was replaced with the existing XPG crystal structure PDB 3Q8K.
Source: Figshare
Authors: Fu, Iwen, E Geacintov, Nicholas, Broyde, Suse
Language: English
Topic: DNA Repair Mechanisms
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4394488299