# ############################################################################################## # PyMOL script for display of the cauliflower (Brassica oleracea var. botrytis) 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: 03/26/2024 # # 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 # # Citation for structure: # # Nature Plants 6, 377–383 (2020) # Cryo-EM structure of the RNA-rich plant mitochondrial ribosome. # Waltz F, Soufari H, Bochler A, Giegé P, Hashem Y # # 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) # # An updated nomenclature for plant ribosomal protein genes. # Scarpin MR, Busche M, Martinez RE, Harper LC, Reiser L, Szakonyi D, Merchante C, Lan T, Xiong W, Mo B, Tang G, Chen X, # Bailey-Serres J, Browning KS, Brunkard JO. # The Plant Cell 35(2):640-643 (2023) # # Abbreviations: # 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) # .....x/y/z suffix indicating the paralog # # ..._temp_.. temporary name, possible renaming currently being discussed # ._ATxxxxxxx Locus identifier for Arabidopsis Genome Initiative (AGI) # # Color Scheme: # light blue: proteins universally conserved # magenta: proteins bacterial-specific # light yellow: proteins mitoribosomal-specific # white: unassigned protein segments # light grey: 26S, 18S and 5S rRNAs # ################ # INSTRUCTIONS # ################ # # 1) Start PyMOL # The structure of the 78S plant 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 6xyw # # 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, ions and cofactors # ######################## # DISPLAY INSTRUCTIONS # ######################## # this matrix superimposes the plant mitochondrial ribosome (6xyw) # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the ASU) cmd.transform_selection("6xyw", [0.5963134306429343, -0.423156306725361, 0.6821649886623895, -24.977800018993932, 0.17643866460342458, 0.8980919502405554, 0.4028651751683313, -356.34493452830225, -0.7831217678419238, -0.1198736200534884, 0.6102053681494042, 274.5198337717545, 0.0, 0.0, 0.0, 1.0],homogenous=1) ############## # SELECTIONS # ############## ### small subunit ############################# create 18S_rRNA, 6xyw and chain 2 create uS2m___AT3G03600, 6xyw and chain Ba create uS3m___ATMG00090, 6xyw and chain Bb create uS4m___ATMG00290, 6xyw and chain Bc create uS5m___AT1G64880, 6xyw and chain Bd create bS6m___AT3G18760, 6xyw and chain Be create uS7m___ATMG01270, 6xyw and chain Bf create uS8my__AT4G29430, 6xyw and chain Bg create uS9m___AT3G49080, 6xyw and chain Bh create uS10m__AT3G22300, 6xyw and chain Bi create uS11m__AT1G31817, 6xyw and chain Bj create uS12m__ATMG00980, 6xyw and chain Bk create uS13m__AT1G77750, 6xyw and chain Bl create uS14m__AT2G34520, 6xyw and chain Bm create uS15mz_AT1G15810, 6xyw and chain Bn create bS16m__AT5G56940, 6xyw and chain Bo create uS17m__AT1G49400, 6xyw and chain Bp create bS18m__AT1G07210, 6xyw and chain Bq create uS19m__AT5G47320, 6xyw and chain Br create bS21m__AT3G26360, 6xyw and chain Bs create bTHXm__AT2G21290, 6xyw and chain Bt create mS23___AT1G26750, 6xyw and chain Bu create mS26___AT5G49210, 6xyw and chain Bv create mS29___AT1G16870, 6xyw and chain Bw create mS33___AT5G44710, 6xyw and chain Bx create mS34___AT5G52370, 6xyw and chain By create mS35z__AT3G18240, 6xyw and chain Bz create mS37___AT1G47278, 6xyw and chain BA create mS38___AT5G63150, 6xyw and chain BB create mS41___AT5G26800, 6xyw and chain BC create mS75_temp_AT5G62270, 6xyw and chain BD create mS47___AT4G31810, 6xyw and chain BE create mS80_rPPR6__AT3G02650, 6xyw and chain BG create mS83_rPPR10_AT4G15640, 6xyw and chain BH ### ssu unassigned ### create mS46_like_unassigned , 6xyw and chain BF create rPPR_like_unassigned1, 6xyw and chain BI create rPPR_like_unassigned2, 6xyw and chain BJ create rPPR_like_unassigned3, 6xyw and chain BK create ssu_unknown1, 6xyw and chain BL create ssu_unknown2, 6xyw and chain BM create ssu_unknown3, 6xyw and chain BN create ssu_unknown4, 6xyw and chain BO create ssu_unknown5, 6xyw and chain BP ### large subunit ############################# create 26S_rRNA, 6xyw and chain 1 create 5S__rRNA, 6xyw and chain 3 create uL2mz_Nter_ATMG00560, 6xyw and chain Aa create uL2my_Cter_AT2G44065, 6xyw and chain Ab create uL3m___AT3G17465, 6xyw and chain Ac create uL4m___AT2G20060, 6xyw and chain Ad create uL5m___ATMG00210, 6xyw and chain Ae create uL6m___AT2G18400, 6xyw and chain Af create bL9m___AT5G53070, 6xyw and chain Ag create uL10m__AT3G12370, 6xyw and chain Ah create uL11m__AT4G35490, 6xyw and chain Ai create uL13m__AT3G01790, 6xyw and chain Aj create uL14m__AT5G46160, 6xyw and chain Ak create uL15m__AT5G64670, 6xyw and chain Al create uL16m__ATMG00080, 6xyw and chain Am create bL17mz_AT5G09770, 6xyw and chain An create uL18m__AT5G27820, 6xyw and chain Ao create bL19m__AT1G24240, 6xyw and chain Ap create bL20m__AT1G16740, 6xyw and chain Aq create bL21m__AT4G30930, 6xyw and chain Ar create uL22mz_AT1G52370, 6xyw and chain As create uL23m__AT4G39880, 6xyw and chain At create uL24m__AT5G23535, 6xyw and chain Au create bL25my_AT5G66860, 6xyw and chain Av create bL27m__AT2G16930, 6xyw and chain Aw create bL28m__AT4G31460, 6xyw and chain Ax create uL29m__AT1G07830, 6xyw and chain Ay create uL30m__AT5G55140, 6xyw and chain Az create bL31my_AT5G55125, 6xyw and chain AA create bL32m__AT1G26740, 6xyw and chain AB create bL33m__AT5G18790, 6xyw and chain AC create bL35m__AT5G45590, 6xyw and chain AD create bL36m__AT5G20180, 6xyw and chain AE create mL40___AT4G05400, 6xyw and chain AF create mL41y__AT5G40080, 6xyw and chain AG create mL43___AT3G59650, 6xyw and chain AH create mL46___AT1G14620, 6xyw and chain AI create mL53___AT5G39600, 6xyw and chain AJ create mS82___temp_AT4G22000, 6xyw and chain AK create bL31mz_temp_AT1G27435, 6xyw and chain AL create mL101_rPPR4_AT1G60770, 6xyw and chain AO create mL102_rPPR5_AT2G37230, 6xyw and chain AP create mL104_rPPR9_AT5G60960, 6xyw and chain AQ create mL105_temp_AT3G51010, 6xyw and chain AN create mL106_temp_AT1G73940, 6xyw and chain AM ### lsu unassigned ### create lsu_unknown1, 6xyw and chain AR ### temporary selections ### select rRNAs , *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)) #################### # DISPLAY SETTINGS # #################### ### coloring ### color grey60, *rRNA color aquamarine, uS* or uL* color violet, bS* or bL* color paleyellow, mS* or mL* color paleyellow, *unassigned* color white, *unknown* color white, bases hide everything ### cartoon settings ### show cartoon, *rRNA show cartoon, uS* or uL* or bS* or bL* or mS* or mL* or *unassigned* or *unknown* 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 delete 6xyw delete rRNAs delete bases ### side view of the 55S ### ###### set_view (\ -0.987847030, 0.021754943, 0.153153449,\ 0.034389943, -0.934180319, 0.354742438,\ 0.150809333, 0.355729073, 0.922201931,\ 0.040274382, -0.029247642, -1087.138793945,\ 216.104431152, 8.003974915, 220.410369873,\ 913.891784668, 1253.049804688, -20.000000000 ) ######