Computational protocol: The indispensable N-terminal half of eIF3j/HCR1 co-operates with itsstructurally conserved binding partner eIF3b/PRT1-RRM and eIF1A in stringent AUGselection

Similar protocols

Protocol publication

[…] The structure of the heIF3b-RRM/heIF3j35-69 peptide complex was calculated using the program CYANA . 1853 NOE-based distances derived from 3D heteronuclear NOESY experiments as well as 113 dihedral angle restraints (Φ and ψ) obtained by analysis of N, Hα, Cα, and Cβ chemical shift values using the TALOS program ; were used in the structure calculations. A total of seven iterations for structural calculations and distance restraint assignment were run with CYANA. 100 structures were calculated, and the 10 structures having the lowest energies were adopted. These structures were then water refined in a minimization run using the SANDER module of AMBER 9.0 . The quality of each structure was assessed using the program Procheck-NMR . A list of all restraints and structural statistics is presented in . Figures were prepared using the programs PyMOL (http://pymol.sourceforge.net/) and MOLMOL . […]

Pipeline specifications

Software tools CYANA, PROCHECK, PyMOL, MOLMOL
Applications NMR-based proteomics analysis, Protein structure analysis
Organisms Saccharomyces cerevisiae, Homo sapiens