# ########################################################## # PyMOL script for display of the yeast 74S mitoribosome # ########################################################## # # 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 # https://bangroup.ethz.ch/research/nomenclature-of-ribosomal-proteins.html # # Reference: # The structure of the yeast mitochondrial ribosome. # Desai N, Brown A, Amunts A, Ramakrishnan V. # Science 355 (6324):528-531 (2017) # # 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):165-169 (2014) # # Structure and Function of the Mitochondrial Ribosome. # Greber BJ, Ban N. # Annu Rev Biochem. 85:103-32 (2016) # # Abbreviations: # S.c. Saccharomyces cerevisiae # uS..m/uL..m mitochondrial version of universally conserved proteins (eukaryotes, archaea and bacteria) # bS..m/bL..m mitochondrial version of bacterial-specific proteins # mS../mL.. mitochondrial-specific proteins (may differ between species) # # Color scheme: # blue: proteins universally conserved # magenta: proteins bacterial-specific # light yellow: proteins mitoribosomal-specific # white: unassigned protein segments # light grey: 21S and 15S rRNAs # dark blue: E-site tRNA # green spheres: magnesium ions # red spheres: water # grey spheres: Zn ions # purple: Na ions # white sticks: GDP bound to mS29 ################ # INSTRUCTIONS # ################ # # 1) Start PyMOL # The structure of the 74S yeast mitoribosome 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 5mrc # # 3) Wait until the file is loaded and you can see the mitoribosome 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 and ions # ######################## # DISPLAY INSTRUCTIONS # ######################## # to activate differentiation between lowercase and uppercase chain IDs used for large molecules # this matrix superimposes the mitochondrial 54S large ribosomal subunit from S. cerevisiae (5mrc) # onto the large cytosolic subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the ASU) cmd.transform_selection("5mrc", [-0.7240350246429443, 0.604046106338501, 0.33301883935928345, 141.81306031409622, 0.591437041759491, 0.7921079397201538, -0.15088802576065063, -276.6505160710458, -0.35493019223213196, 0.08771147578954697, -0.930769145488739, 512.8526183051634, 0.0, 0.0, 0.0, 1.0],homogenous=1) ############## # SELECTIONS # ############## ### temporary subselections ### create 5mrc_cofactors, 5mrc and (resn MG or resn ZN or resn NA or resn GDP) create 5mrc_wo_cofactors, 5mrc and not (resn MG or resn ZN or resn NA or resn GDP) delete 5mrc ########################### 54S LSU ################################ ### 54S rRNA and tRNA ### create 21S___S.c.rRNA , 5mrc_wo_cofactors and chain A create Esite_S.c.tRNA , 5mrc_wo_cofactors and chain bb ### 54S proteins ### create uL2m__S.c.RML2 , 5mrc_wo_cofactors and chain B create uL3m__S.c.MRPL9 , 5mrc_wo_cofactors and chain C create uL4m__S.c.YML6 , 5mrc_wo_cofactors and chain D create uL5m__S.c.MRPL7 , 5mrc_wo_cofactors and chain E create uL6m__S.c.MRPL6 , 5mrc_wo_cofactors and chain F create bL9m__S.c.MRPL50 , 5mrc_wo_cofactors and chain G create uL13m_S.c.MRPL23 , 5mrc_wo_cofactors and chain H create uL14m_S.c.MRPL38_MRPL34 , 5mrc_wo_cofactors and chain I create uL15m_S.c.MRPL10_MRPL18 , 5mrc_wo_cofactors and chain J create uL16m_S.c.MRPL16_RML16 , 5mrc_wo_cofactors and chain K create bL17m_S.c.MRPL8 , 5mrc_wo_cofactors and chain L create bL19m_S.c.IMG1_PETCR46 , 5mrc_wo_cofactors and chain M create bL21m_S.c.MRPL49 , 5mrc_wo_cofactors and chain N create uL22m_S.c.MRPL22 , 5mrc_wo_cofactors and chain O create uL23m_S.c.MRP20_MRPL41 , 5mrc_wo_cofactors and chain P create uL24m_S.c.MRPL40 , 5mrc_wo_cofactors and chain Q create bL27m_S.c.MRP7_MRPL2 , 5mrc_wo_cofactors and chain R create bL28m_S.c.MRPL24_MRPL14 , 5mrc_wo_cofactors and chain S create uL29m_S.c.MRPL4 , 5mrc_wo_cofactors and chain T create uL30m_S.c.MRPL33 , 5mrc_wo_cofactors and chain U create bL31m_S.c.MRPL36 , 5mrc_wo_cofactors and chain V create bL32m_S.c.MRPL32 , 5mrc_wo_cofactors and chain W create bL33m_S.c.MRPL39 , 5mrc_wo_cofactors and chain X create bL34m_S.c.MRPL34 , 5mrc_wo_cofactors and chain Y create bL35m_S.c.YNL122C , 5mrc_wo_cofactors and chain Z create bL36m_S.c.RTC6_TAE4 , 5mrc_wo_cofactors and chain 0 create mL38__S.c.MRPL35 , 5mrc_wo_cofactors and chain 1 create mL40__S.c.MRPL28 , 5mrc_wo_cofactors and chain 2 create mL41__S.c.MRPL27 , 5mrc_wo_cofactors and chain 3 create mL43__S.c.MRPL51 , 5mrc_wo_cofactors and chain 4 create mL44__S.c.MRPL3 , 5mrc_wo_cofactors and chain 5 create mL46__S.c.MRPL17_MRPL30 , 5mrc_wo_cofactors and chain 6 create mL49__S.c.IMG2 , 5mrc_wo_cofactors and chain 7 create mL50__S.c.MRPL13 , 5mrc_wo_cofactors and chain 8 create mL57__S.c.MRPL15 , 5mrc_wo_cofactors and chain 9 create mL58__S.c.MRPL20 , 5mrc_wo_cofactors and chain a create mL59__S.c.MRPL25_YMR26 , 5mrc_wo_cofactors and chain b create mL60__S.c.MRPL31 , 5mrc_wo_cofactors and chain c create mL67__S.c.MHR1_XTC1 , 5mrc_wo_cofactors and chain d # 54S cofactors # create 54S_Mg , 5mrc_cofactors and name MG and not (chain aa or chain BB or chain NN or chain MM or chain QQ or chain WW) create bL32m_Zn , 5mrc_cofactors and chain W create bL36m_Zn , 5mrc_cofactors and chain 0 create uL2m_Na , 5mrc_cofactors and chain B ########################### 37S SSU ################################ ### 37S rRNA ### create 15S___S.c.rRNA , 5mrc_wo_cofactors and chain aa # 37S proteins # create bS1m__S.c.MRP51 , 5mrc_wo_cofactors and chain AA create uS2m__S.c.MRP4_MRP4A , 5mrc_wo_cofactors and chain BB create uS3m__S.c.VAR1 , 5mrc_wo_cofactors and chain CC create uS4m__S.c.NAM9_MNA6 , 5mrc_wo_cofactors and chain DD create uS5m__S.c.MRPS5 , 5mrc_wo_cofactors and chain EE create bS6m__S.c.MRP17 , 5mrc_wo_cofactors and chain FF create uS7m__S.c.RSM7 , 5mrc_wo_cofactors and chain GG create uS8m__S.c.MRPS8 , 5mrc_wo_cofactors and chain HH create uS9m__S.c.MRPS9 , 5mrc_wo_cofactors and chain II create uS10m_S.c.RSM10 , 5mrc_wo_cofactors and chain JJ create uS11m_S.c.MRPS18 , 5mrc_wo_cofactors and chain KK create uS12m_S.c.MRPS12 , 5mrc_wo_cofactors and chain LL create uS13m_S.c.SWS2 , 5mrc_wo_cofactors and chain MM create uS14m_S.c.MRP2 , 5mrc_wo_cofactors and chain NN create uS15m_S.c.MRPS28 , 5mrc_wo_cofactors and chain OO create bS16m_S.c.MRPS16 , 5mrc_wo_cofactors and chain PP create uS17m_S.c.MRPS17 , 5mrc_wo_cofactors and chain QQ create bS18m_S.c.RSM18 , 5mrc_wo_cofactors and chain RR create uS19m_S.c.RSM19 , 5mrc_wo_cofactors and chain SS create bS21m_S.c.MRP21_MRP50 , 5mrc_wo_cofactors and chain TT create mS23__S.c.RSM25 , 5mrc_wo_cofactors and chain UU create mS26__S.c.PET123 , 5mrc_wo_cofactors and chain VV create mS29__S.c.RSM23 , 5mrc_wo_cofactors and chain WW create mS33__S.c.RSM27 , 5mrc_wo_cofactors and chain XX create mS35__S.c.RSM24 , 5mrc_wo_cofactors and chain YY create mS37__S.c.MRP10 , 5mrc_wo_cofactors and chain ZZ create mS38__S.c.QRI5_COX24 , 5mrc_wo_cofactors and chain 11 create mS41__S.c.FYV4 , 5mrc_wo_cofactors and chain 22 create mS42__S.c.RSM26 , 5mrc_wo_cofactors and chain 33 create mS43__S.c.MRP1 , 5mrc_wo_cofactors and chain 44 create mS44__S.c.MRP13 , 5mrc_wo_cofactors and chain 55 create mS45__S.c.MRPS35 , 5mrc_wo_cofactors and chain 66 create mS46__S.c.RSM28 , 5mrc_wo_cofactors and chain 77 create mS47__S.c.EHD3_MRP5 , 5mrc_wo_cofactors and chain 88 create unassigned_37S_head_protein , 5mrc_wo_cofactors and chain cc create unassigned_37S_body_protein , 5mrc_wo_cofactors and chain dd ### 37S cofactors ### create 37S_Mg , 5mrc_cofactors and name MG and (chain aa or chain BB or chain NN or chain MM or chain QQ or chain WW) create mS29_Mg_GDP , 5mrc_cofactors and chain WW delete 5mrc_cofactors delete 5mrc_wo_cofactors #################### # DISPLAY SETTINGS # #################### ### temporary subselections ### select rRNAs, 21S___S.c.rRNA or 15S___S.c.rRNA 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 white, bases color density, Esite_S.c.tRNA color aquamarine, uS* or uL* color violet, bS* or bL* color paleyellow, mS* or mL* color white, unassigned* color white, mS29_Mg_GDP util.cnc mS29_Mg_GDP color yellow, bL32m_Zn or bL36m_Zn util.cnc uL2m_Na util.cnc 37S_Mg or 54S_Mg or (mS29_Mg_GDP and name MG) delete bases delete rRNAs hide everything ### cartoon settings ### show cartoon, 21S___S.c.rRNA or 15S___S.c.rRNA or Esite_S.c.tRNA show cartoon, uS* or uL* or bS* or bL* or mS* or mL* or unassigned* 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, bL32m_Zn or bL36m_Zn or uL2m_Na or 37S_Mg or 54S_Mg or (mS29_Mg_GDP and name MG) show sticks, mS29_Mg_GDP and resn GDP set stick_radius=0.4 set sphere_scale=0.5 /cmd.set('valence',0,u'',0) ### side view of the 74S ### set_view (\ -0.987847030, 0.021754943, 0.153153449,\ 0.034389943, -0.934180319, 0.354742438,\ 0.150809333, 0.355729073, 0.922201931,\ 0.032001138, -0.028823834, -889.626464844,\ 181.108840942, 7.865180969, 228.375671387,\ 742.704956055, 1033.084594727, -20.000000000 ) ######