Computational protocol: Structural basis of mRNA cap recognition by Dcp1–Dcp2

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Protocol publication

[…] All data were collected at Lawrence Berkeley National Lab, Beamline 8.3.1 at the Advanced Light Source on an ADSC Quantum 315r CCD detector at 100 K and a wavelength of 1.115869 Å. Data were indexed, integrated and scaled using HKL2000. The structures were solved in space group P21 by molecular replacement using Phaser in the CCP4 suite. We used chains A and B of PDB 2QKM as a molecular replacement model, first placing Dcp1–Dcp2(1-94), then Dcp2(95-243). After a preliminary round of refinement including rigid-body refinement in PHENIX, the structure was manually adjusted in COOT and iteratively refined in PHENIX. Final refinements used Non-Crystallographic Symmetry (NCS), Translation-Libration-Screw-rotation (TLS), stereochemical, and Atomic Displacement Parameter (ADP) restraints. For the final model of Dcp1–scPNRC2Dcp2, all residues were in the favored (92.7%), allowed (6.8%), or generously allowed (0.4%), regions of the Ramachandran plot generated by ProCheck, with none disallowed. For the final model of Dcp1–scPNRC2Dcp2 with two-headed cap analog bound, a single residue was in the disallowed region of the Ramachandran plot generated by ProCheck (0.1%, D91 chain D), with the remaining residues falling within the favored (92%), allowed (7.7%), or generously allowed (0.1%) regions.All structural figures were prepared using PyMol version 1.7. Electrostatic surfaces were calculated using PDB2PQR & APBS webservers,, using the AMBER94 forcefield to calculate charges. Electrostatic surfaces were visualized in PyMol using APBS tools 2.1. […]

Pipeline specifications

Software tools CCP4, PHENIX, Coot, PROCHECK, PyMOL, PDB2PQR
Application Protein structure analysis
Organisms Schizosaccharomyces pombe, Homo sapiens
Chemicals Nucleotides