MD package of wtXPD-damaged-ssDNA

MD simulation: wtXPD-damaged-ssDNA

XPD-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.pdb

XPG-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.