# ############################################################ # PyMOL script for display of the chloroplast 70S ribosome # ############################################################ # # Created by Marc Leibundgut, ETH Zurich. # For questions, error reports and comments please contact ban@mol.biol.ethz.ch or leibundgut@mol.biol.ethz.ch # # last modified: 04/02/2024 # # A full PyMOL session of this script in .pse format can be downloaded from # http://www.bangroup.ethz.ch/research/nomenclature-of-ribosomal-proteins.html # # Reference: # The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. # Philipp Bieri, Marc Leibundgut, Martin Saurer, Daniel Boehringer, Nenad Ban # The EMBO Journal, doi: 10.15252/embj.201695959. # # Nomenclature according to: # A new system for naming ribosomal proteins. # Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, Lafontaine DL, Lindahl L, Liljas A, Lipton JM, McAlear MA, # Moore PB, Noller HF, Ortega J, Panse VG, Ramakrishnan V, Spahn CM, Steitz TA, Tchorzewski M, Tollervey D, Warren AJ, # Williamson JR, Wilson D, Yonath A, Yusupov M. # Curr Opin Struct Biol. 24:165-9 (2014) # # Abbreviations: # uS..c/uL..c chloroplast version of universally conserved proteins (eukaryotes, archaea and bacteria) # bS..c/bL..c chloroplast version of bacterial-specific proteins # cS../cL.. chloroplast-specific proteins (may differ between species) # # Color Scheme: # blue: proteins universally conserved # magenta: proteins bacterial-specific # light yellow: proteins chloroplast-specific # light grey: 23S, 5S, 4.5S and 16S rRNAs # dark blue: translation factor plastid pY and E-site tRNA # grey spheres: zinc ions # green spheres: magnesium ions # ################ # INSTRUCTIONS # ################ # # # 1) Start PyMOL # The structure of the chloroplast 70S ribosome has been deposited at the PDB in mmCIF format. Only recent versions # of PyMOL can properly retrieve and handle files in mmCIF format. If you do not have a recent version of PyMOL # installed (this script has been tested with PyMOL v2.2.5 and may not work properly with older versions), # please go to http://www.pymol.org/ to download and install the application. # # 2) The following command will download the PDB coordinate file from the database and save it in your working # directory. To load the file, paste the command into the command line of the PyMOL GUI Window # (titled "The Pymol Molecular Graphics System") # fetch 5mmm # # 3) Wait until the file is loaded and you can see the chloroplast 70S ribosome shown as lines. # # 4) Paste the rest of the script below "DISPLAY INSTRUCTIONS" into the command line of # the PyMOL GUI Window (titled "The Pymol Molecular Graphics System") # These commands will set up the display and nomenclature of RNAs, proteins, ions and cofactors # ######################## # DISPLAY INSTRUCTIONS # ######################## # the following matrix superimposes the chloroplast 70S ribosome from S. oleracea (5mmm) # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the asymmetric unit) cmd.transform_selection("5mmm", [-0.7544724941253662, -0.6557680368423462, -0.02719421312212944, 500.4582675533463, 0.30964356660842896, -0.31910598278045654, -0.8957076668739319, 202.72973252134852, 0.5786986351013184, -0.6842073202133179, 0.4438110291957855, 160.6443022802364, 0.0, 0.0, 0.0, 1.0],homogenous=1) ############## # SELECTIONS # ############## ### temporary subselections ### create 5mmm_cofactors, 5mmm and (resn MG or resn ZN) create 5mmm_wo_cofactors, 5mmm and not (resn MG or resn ZN) delete 5mmm ### chloroplast 30S ### create 16SrRNA, 5mmm_wo_cofactors and chain a create EtRNA, 5mmm_wo_cofactors and chain z create bS1c, 5mmm_wo_cofactors and chain 8 create uS2c, 5mmm_wo_cofactors and chain b create uS3c, 5mmm_wo_cofactors and chain c create uS4c, 5mmm_wo_cofactors and chain d create uS5c, 5mmm_wo_cofactors and chain e create bS6c, 5mmm_wo_cofactors and chain f create uS7c, 5mmm_wo_cofactors and chain g create uS8c, 5mmm_wo_cofactors and chain h create uS9c, 5mmm_wo_cofactors and chain i create uS10c, 5mmm_wo_cofactors and chain j create uS11c, 5mmm_wo_cofactors and chain k create uS12c, 5mmm_wo_cofactors and chain l create uS13c, 5mmm_wo_cofactors and chain m create uS14c, 5mmm_wo_cofactors and chain n create uS15c, 5mmm_wo_cofactors and chain o create bS16c, 5mmm_wo_cofactors and chain p create uS17c, 5mmm_wo_cofactors and chain q create bS18c, 5mmm_wo_cofactors and chain r create uS19c, 5mmm_wo_cofactors and chain s create bS20c, 5mmm_wo_cofactors and chain t create bS21c, 5mmm_wo_cofactors and chain u create cS22, 5mmm_wo_cofactors and chain v create cS23, 5mmm_wo_cofactors and chain w create bTHXc, 5mmm_wo_cofactors and chain x create pY, 5mmm_wo_cofactors and chain y ### chloroplast 50S ### create 23SrRNA, 5mmm_wo_cofactors and chain A create 5SrRNA, 5mmm_wo_cofactors and chain B create 4SrRNA, 5mmm_wo_cofactors and chain W create uL2c, 5mmm_wo_cofactors and chain C create uL3c, 5mmm_wo_cofactors and chain D create uL4c, 5mmm_wo_cofactors and chain E create uL5c, 5mmm_wo_cofactors and chain F create uL6c, 5mmm_wo_cofactors and chain G create bL9c, 5mmm_wo_cofactors and chain H create uL10c, 5mmm_wo_cofactors and chain I create uL11c, 5mmm_wo_cofactors and chain J create uL13c, 5mmm_wo_cofactors and chain K create uL14c, 5mmm_wo_cofactors and chain L create uL15c, 5mmm_wo_cofactors and chain M create uL16c, 5mmm_wo_cofactors and chain N create bL17c, 5mmm_wo_cofactors and chain O create uL18c, 5mmm_wo_cofactors and chain P create bL19c, 5mmm_wo_cofactors and chain Q create bL20c, 5mmm_wo_cofactors and chain R create bL21c, 5mmm_wo_cofactors and chain S create uL22c, 5mmm_wo_cofactors and chain T create uL23c, 5mmm_wo_cofactors and chain U create uL24c, 5mmm_wo_cofactors and chain V create bL27c, 5mmm_wo_cofactors and chain X create bL28c, 5mmm_wo_cofactors and chain Y create uL29c, 5mmm_wo_cofactors and chain Z create bL31c, 5mmm_wo_cofactors and chain 0 create bL32c, 5mmm_wo_cofactors and chain 1 create bL33c, 5mmm_wo_cofactors and chain 2 create bL34c, 5mmm_wo_cofactors and chain 3 create bL35c, 5mmm_wo_cofactors and chain 4 create bL36c, 5mmm_wo_cofactors and chain 5 create cL37, 5mmm_wo_cofactors and chain 6 create cL38, 5mmm_wo_cofactors and chain 7 delete 5mmm_wo_cofactors ### chloroplast 70S cofactors ### create 70S_Mg, 5mmm_cofactors and resn MG create 70S_Zn, 5mmm_cofactors and resn ZN delete 5mmm_cofactors #################### # DISPLAY SETTINGS # #################### ### temporary subselections ### select rRNAs, 23SrRNA or 5SrRNA or 4SrRNA or 16SrRNA select bases, (rRNAs and (name C4 or name N3 or name N9 or name C8 or name N7 or name C5 or name C6 or name N1 or name N6 or name C2 or name O2 or name O4 or name O6 or name N2 or name N4)) ### coloring ### color grey60, rRNAs color density, EtRNA color white, bases color aquamarine, uS* or uL* color violet, bS* or bL* or bTHXc color green, cS* or cL* color density, pY util.cnc 70S_Zn util.cnc 70S_Mg delete bases delete rRNAs hide everything # cartoon settings # show cartoon, 23SrRNA or 5SrRNA or 4SrRNA or 16SrRNA or EtRNA show cartoon, uS* or uL* or bS* or bL* or cS* or cL* or bTHXc or pY set cartoon_loop_radius,0.40000 set cartoon_tube_radius,0.8000 set cartoon_ladder_radius,0.4000 set cartoon_oval_length,1.200 set cartoon_oval_width,0.4000 show spheres, 70S_Mg show spheres, 70S_Zn set sphere_scale=0.5 ### side view of the 70S ### set_view (\ -0.987847030, 0.021754943, 0.153153449,\ 0.034389943, -0.934180319, 0.354742438,\ 0.150809333, 0.355729073, 0.922201931,\ 0.032189518, -0.031000840, -888.531250000,\ 181.439712524, 1.238510132, 232.057281494,\ 742.704956055, 1033.084594727, -20.000000000 ) ######