# ############################################################ # PyMOL script for display of the porcine 55S 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 # # Nature 560 (7717):263-267. (2018) # Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. # Kummer E, Leibundgut M, Rackham O, Lee RG, Boehringer D, Filipovska A, Ban N. # # 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: # 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: 12S and 16S rRNAs, CP-tRNA # dark blue: P-site fMet-tRNA(Met), mRNA, mtIF2 # green spheres: magnesium ions # red spheres: water # grey spheres: Zn ions # purple: Na ion # white sticks: other cofactors (GTP and GTPgS bound to mS29 and mtIF2, formyl-methionine linked to tRNA(Met), spermines and GMPs # ################ # INSTRUCTIONS # ################ # # 1) Start PyMOL # The structure of the 55S 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 6gaw # # 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 55S mitochondrial ribosome from S. scrofa (6gaw) # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the ASU) cmd.transform_selection("6gaw", [-0.7333857417106628, -0.5194918513298035, -0.4384901523590088, 503.4812669414987, 0.37349313497543335, -0.8468506932258606, 0.37861168384552, 19.46779491758025, -0.5680213570594788, 0.11389534175395966, 0.8150948286056519, 172.1365059939485, 0.0, 0.0, 0.0, 1.0],homogenous=1) ############## # SELECTIONS # ############## ### temporary subselections ### create 6gaw_cofactors, 6gaw and (resn MG or resn NA or resn HOH or resn ZN or resn GTP or resn GSP or resn 5GP or resn SPM or resn FME) create 6gaw_wo_cofactors, 6gaw and not (resn MG or resn NA or resn HOH or resn ZN or resn GTP or resn GSP or resn 5GP or resn SPM or resn FME) delete 6gaw ### 28S small mitoribosomal_subunit ### create 12S_rRNA, 6gaw_wo_cofactors and chain AA create Psite_tRNA_Met, 6gaw_wo_cofactors and chain AV create MT-CO3_mRNA, 6gaw_wo_cofactors and chain AX create bS1m__MRPS28, 6gaw_wo_cofactors and chain Af create uS2m__MRPS2, 6gaw_wo_cofactors and chain AB create uS3m__MRPS24, 6gaw_wo_cofactors and chain AC create uS5m__MRPS5, 6gaw_wo_cofactors and chain AE create bS6m__MRPS6, 6gaw_wo_cofactors and chain AF create uS7m__MRPS7, 6gaw_wo_cofactors and chain AG create uS9m__MRPS9, 6gaw_wo_cofactors and chain AI create uS10m_MRPS10, 6gaw_wo_cofactors and chain AJ create uS11m_MRPS11, 6gaw_wo_cofactors and chain AK create uS12m_MRPS12, 6gaw_wo_cofactors and chain AL create uS14m_MRPS14, 6gaw_wo_cofactors and chain AN create uS15m_MRPS15, 6gaw_wo_cofactors and chain AO create bS16m_MRPS16, 6gaw_wo_cofactors and chain AP create uS17m_MRPS17, 6gaw_wo_cofactors and chain AQ create bS18m_MRPS18C, 6gaw_wo_cofactors and chain AR create bS21m_MRPS21, 6gaw_wo_cofactors and chain AU create mS22__MRPS22, 6gaw_wo_cofactors and chain Aa create mS23__MRPS23, 6gaw_wo_cofactors and chain Ab create mS25__MRPS25, 6gaw_wo_cofactors and chain Ac create mS26__MRPS26, 6gaw_wo_cofactors and chain Ad create mS27__MRPS27, 6gaw_wo_cofactors and chain Ae create mS29__MRPS29_DAP3, 6gaw_wo_cofactors and chain Ag create mS31__MRPS31, 6gaw_wo_cofactors and chain Ah create mS33__MRPS33, 6gaw_wo_cofactors and chain Ai create mS34__MRPS34, 6gaw_wo_cofactors and chain Aj create mS35__MRPS35, 6gaw_wo_cofactors and chain Ak create mS37__MRPS37_CHCHD1, 6gaw_wo_cofactors and chain Am create mS38__MRPS38_AURKAIP1, 6gaw_wo_cofactors and chain An create mS39__MRPS39_PTCD3, 6gaw_wo_cofactors and chain Ao create mS40__MRPS18B, 6gaw_wo_cofactors and chain Ap create unassigned_28S_head_protein, 6gaw_wo_cofactors and chain AZ ### 39S large mitoribosomal subunit ### create 16S_rRNA, 6gaw_wo_cofactors and chain BA create CP_tRNA_Phe, 6gaw_wo_cofactors and chain BB create uL2m__MRPL2, 6gaw_wo_cofactors and chain BD create uL3m__MRPL3, 6gaw_wo_cofactors and chain BE create uL4m__MRPL4, 6gaw_wo_cofactors and chain BF create bL9m__MRPL9, 6gaw_wo_cofactors and chain BI create uL10m_MRPL10, 6gaw_wo_cofactors and chain BJ create uL11m_MRPL11, 6gaw_wo_cofactors and chain BK create bL12m_MRPL12, 6gaw_wo_cofactors and (chain BL or chain CL or chain DL or chain EL or chain FL or chain GL or chain HL) create uL13m_MRPL13, 6gaw_wo_cofactors and chain BN create uL14m_MRPL14, 6gaw_wo_cofactors and chain BO create uL15m_MRPL15, 6gaw_wo_cofactors and chain BP create uL16m_MRPL16, 6gaw_wo_cofactors and chain BQ create bL17m_MRPL17, 6gaw_wo_cofactors and chain BR create uL18m_MRPL18, 6gaw_wo_cofactors and chain BS create bL19m_MRPL19, 6gaw_wo_cofactors and chain BT create bL20m_MRPL20, 6gaw_wo_cofactors and chain BU create bL21m_MRPL21, 6gaw_wo_cofactors and chain BV create uL22m_MRPL22, 6gaw_wo_cofactors and chain BW create uL23m_MRPL23, 6gaw_wo_cofactors and chain BX create uL24m_MRPL24, 6gaw_wo_cofactors and chain BY create bL27m_MRPL27, 6gaw_wo_cofactors and chain B0 create bL28m_MRPL28, 6gaw_wo_cofactors and chain B1 create uL29m_MRPL47, 6gaw_wo_cofactors and chain B2 create uL30m_MRPL30, 6gaw_wo_cofactors and chain B3 create bL31m_MRPL55, 6gaw_wo_cofactors and chain B4 create bL32m_MRPL32, 6gaw_wo_cofactors and chain B5 create bL33m_MRPL33, 6gaw_wo_cofactors and chain B6 create bL34m_MRPL34, 6gaw_wo_cofactors and chain B7 create bL35m_MRPL35, 6gaw_wo_cofactors and chain B8 create bL36m_MRPL36, 6gaw_wo_cofactors and chain B9 create mL37__MRPL37, 6gaw_wo_cofactors and chain Ba create mL38__MRPL38, 6gaw_wo_cofactors and chain Bb create mL39__MRPL39, 6gaw_wo_cofactors and chain Bc create mL40__MRPL40, 6gaw_wo_cofactors and chain Bd create mL41__MRPL41, 6gaw_wo_cofactors and chain Be create mL42__MRPL42, 6gaw_wo_cofactors and chain Bf create mL43__MRPL43, 6gaw_wo_cofactors and chain Bg create mL44__MRPL44, 6gaw_wo_cofactors and chain Bh create mL45__MRPL45, 6gaw_wo_cofactors and chain Bi create mL46__MRPL46, 6gaw_wo_cofactors and chain Bj create mL48__MRPL48, 6gaw_wo_cofactors and chain Bk create mL49__MRPL49, 6gaw_wo_cofactors and chain Bl create mL50__MRPL50, 6gaw_wo_cofactors and chain Bm create mL51__MRPL51, 6gaw_wo_cofactors and chain Bn create mL52__MRPL52, 6gaw_wo_cofactors and chain Bo create mL53__MRPL53, 6gaw_wo_cofactors and chain Bp create mL54__MRPL54, 6gaw_wo_cofactors and chain Bq create mL62__MRPL58_ICT1, 6gaw_wo_cofactors and chain Bu create mL63__MRPL57, 6gaw_wo_cofactors and chain Bt create mL64__MRPL59_CRIF1, 6gaw_wo_cofactors and chain Bv create mL65__MRPS30, 6gaw_wo_cofactors and chain Bw create mL66__MRPS18A, 6gaw_wo_cofactors and chain Bx create unassigned_39S_proteins, 6gaw_wo_cofactors and chain Bz create mtIF2, 6gaw_wo_cofactors and chain BC delete 6gaw_wo_cofactors ### 55S cofactors ### create mS29_GTP_Mg_HOH, 6gaw_cofactors and (chain Ag and (resn GTP or resn MG or resn HOH)) create mtIF2_GTPgS_Mg_HOH_Na, 6gaw_cofactors and chain BC and (resn GSP or resn MG or resn HOH or resn NA) create Psite_tRNA_Met_formylmethionine, 6gaw_cofactors and resn FME create 55S_SPM, 6gaw_cofactors and resn SPM create 55S_5GP, 6gaw_cofactors and resn 5GP create 55S_Mg, 6gaw_cofactors and resn MG and not ((chain Ag and (resn GTP or resn MG or resn HOH)) or (chain BC and (resn GSP or resn MG or resn HOH or resn NA))) create 39S_Zn, 6gaw_cofactors and chain B* and resn ZN create 28S_Zn, 6gaw_cofactors and chain A* and resn ZN delete 6gaw_cofactors #################### # DISPLAY SETTINGS # #################### ### temporary subselections ### select rRNAs, 16S_rRNA or CP_tRNA_Phe or 12S_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 density, Psite_tRNA_Met or MT-CO3_mRNA or mtIF2 color white, bases color aquamarine, uS* or uL* color violet, bS* or bL* color paleyellow, mS* or mL* color white, unassigned* color white, mS29_GTP_Mg_HOH, color white, mtIF2_GTPgS_Mg_HOH_Na, color white, Psite_tRNA_Met_formylmethionine util.cnc resn 5GP or resn SPM util.cnc mS29_GTP_Mg_HOH util.cnc mtIF2_GTPgS_Mg_HOH_Na util.cnc Psite_tRNA_Met_formylmethionine util.cnc 39S_Zn or 28S_Zn util.cnc resn MG util.cnc resn HOH util.cnc resn NA delete bases delete rRNAs hide everything ### cartoon settings ### show cartoon, 16S_rRNA or CP_tRNA_Phe or 12S_rRNA or Psite_tRNA_Met or MT-CO3_mRNA show cartoon, uS* or uL* or bS* or bL* or mS* or mL* or unassigned* or mtIF2 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, name MG or name HOH or name ZN or name NA set sphere_scale=0.5 show sticks, 55S_SPM or 55S_5GP or Psite_tRNA_Met_formylmethionine or mtIF2_GTPgS_Mg_HOH_Na or mS29_GTP_Mg_HOH set stick_radius=0.4 /cmd.set('valence',0,u'',0) ### 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,\ 0.032178447, -0.030671358, -889.338989258,\ 181.292022705, 2.002853394, 230.911941528,\ 630.682067871, 1145.107543945, -20.000000000 ) ######