################################################################################## # PyMOL script for display of the 80S ribosome of rabbit (Oryctolagus cuniculus # ################################################################################## # # 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 # https://bangroup.ethz.ch/research/nomenclature-of-ribosomal-proteins.html # # Reference: # # Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. # Bhatt PR, Scaiola A, Loughran G, Leibundgut M, Kratzel A, Meurs R, Dreos R, O'Connor KM, # McMillan A, Bode JW, Thiel V, Gatfield D, Atkins JF, Ban N. # Science 372(6548):1306-1313 (2021) # # 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) # # Abbreviations: # uS../uL.. universally conserved proteins (eukaryotes, archaea and bacteria) # eS../eL.. archaeal- and eukaryotic-specific proteins # # Color Scheme: # blue: proteins universally conserved # orange: proteins conserved in archaea and eukaryotes # red: proteins eukaryotic-specific # dark blue: tRNAs, mRNA and nascent chain # light grey: rRNA # green spheres: magnesium ions # red spheres: water # grey spheres: Zn ions # beige spheres: other ions # ######################################### # INSTRUCTIONS FOR RUNNING THIS SCRIPT # ######################################### # # 1) Start PyMOL # The structure of the O. cuniculus 80S 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 v2.5.5 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") # # to activate distance-based display of bonds to properly show non-standard bases (to be set prior to loading mmCIF) # fetch 7o7y # # 3) Wait until the file is loaded and you can see the ribosome. # # 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 80S rabbit ribosome # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the asymmetric unit) cmd.transform_selection("7o7y", [-0.4334298372268677, -0.7053388357162476, -0.5609239935874939, 677.7894930161983, 0.28932878375053406, 0.48056459426879883, -0.8278566002845764, 19.50137473279574, 0.8534796237945557, -0.5211091637611389, -0.004216201137751341, 138.19158205922082, 0.0, 0.0, 0.0, 1.0],homogenous=1) ################################# # SELECTIONS OF PROTEIN and RNA # ################################# ### 60S proteins, rRNAs and bound nascent chain ### create uL1__L10A_mammalian_80S , 7o7y and chain Bv create uL2__L8___mammalian_80S , 7o7y and chain BA create uL3__L3___mammalian_80S , 7o7y and chain BB create uL4__L4___mammalian_80S , 7o7y and chain BC create uL5__L11__mammalian_80S , 7o7y and chain BJ create uL6__L9___mammalian_80S , 7o7y and chain BH create eL6__L6___mammalian_80S , 7o7y and chain BE create eL8__L7A__mammalian_80S , 7o7y and chain BG create uL10_P0___mammalian_80S , 7o7y and chain Bs create uL11_L12__mammalian_80S , 7o7y and chain Bt create uL13_L13A_mammalian_80S , 7o7y and chain BO create eL13_L13__mammalian_80S , 7o7y and chain BL create uL14_L23__mammalian_80S , 7o7y and chain BV create eL14_L14__mammalian_80S , 7o7y and chain BM create uL15_L27A_mammalian_80S , 7o7y and chain Ba create eL15_L15__mammalian_80S , 7o7y and chain BN create uL16_L10__mammalian_80S , 7o7y and chain BI create uL18_L5___mammalian_80S , 7o7y and chain BD create eL18_L18__mammalian_80S , 7o7y and chain BQ create eL19_L19__mammalian_80S , 7o7y and chain BR create eL20_L18A_mammalian_80S , 7o7y and chain BS create eL21_L21__mammalian_80S , 7o7y and chain BT create uL22_L17__mammalian_80S , 7o7y and chain BP create eL22_L22__mammalian_80S , 7o7y and chain BU create eL24_L24__mammalian_80S , 7o7y and chain BW create uL23_L23A_mammalian_80S , 7o7y and chain BX create uL24_L26__mammalian_80S , 7o7y and chain BY create eL27_L27__mammalian_80S , 7o7y and chain BZ create eL28_L28__mammalian_80S , 7o7y and chain Br create uL29_L35__mammalian_80S , 7o7y and chain Bh create eL29_L29__mammalian_80S , 7o7y and chain Bb create uL30_L7___mammalian_80S , 7o7y and chain BF create eL30_L30__mammalian_80S , 7o7y and chain Bc create eL31_L31__mammalian_80S , 7o7y and chain Bd create eL32_L32__mammalian_80S , 7o7y and chain Be create eL33_L35A_mammalian_80S , 7o7y and chain Bf create eL34_L34__mammalian_80S , 7o7y and chain Bg create eL36_L36__mammalian_80S , 7o7y and chain Bi create eL37_L37__mammalian_80S , 7o7y and chain Bj create eL38_L38__mammalian_80S , 7o7y and chain Bk create eL39_L39__mammalian_80S , 7o7y and chain Bl create eL40_L40__mammalian_80S , 7o7y and chain Bm create eL42_L36A_mammalian_80S , 7o7y and chain Bo create eL43_L37A_mammalian_80S , 7o7y and chain Bp create 28S__rRNA_mammalian_80S , 7o7y and chain B5 create 5S___rRNA_mammalian_80S , 7o7y and chain B7 create 5.8S_rRNA_mammalian_80S , 7o7y and chain B8 create SARS-CoV-2_NC , 7o7y and chain BK ### 40S proteins, rRNA and bound mRNA and tRNAs ### create eS1__S3A__mammalian_80S , 7o7y and chain Aa create uS2__SA___mammalian_80S , 7o7y and chain AZ create uS3__S3___mammalian_80S , 7o7y and chain Ac create uS4__S9___mammalian_80S , 7o7y and chain Ai create eS4__S4___mammalian_80S , 7o7y and chain Ad create uS5__S2___mammalian_80S , 7o7y and chain Ab create eS6__S6___mammalian_80S , 7o7y and chain Af create uS7__S5___mammalian_80S , 7o7y and chain Ae create eS7__S7___mammalian_80S , 7o7y and chain Ag create uS8__S15A_mammalian_80S , 7o7y and chain Av create eS8__S8___mammalian_80S , 7o7y and chain Ah create uS9__S16__mammalian_80S , 7o7y and chain Ap create uS10_S20__mammalian_80S , 7o7y and chain At create eS10_S10__mammalian_80S , 7o7y and chain Aj create uS11_S14__mammalian_80S , 7o7y and chain An create uS12_S23__mammalian_80S , 7o7y and chain Aw create eS12_S12__mammalian_80S , 7o7y and chain Al create uS13_S18__mammalian_80S , 7o7y and chain Ar create uS14_S29__mammalian_80S , 7o7y and chain AG create uS15_S13__mammalian_80S , 7o7y and chain Am create uS17_S11__mammalian_80S , 7o7y and chain Ak create eS17_S17__mammalian_80S , 7o7y and chain Aq create uS19_S15__mammalian_80S , 7o7y and chain Ao create eS19_S19__mammalian_80S , 7o7y and chain As create eS21_S21__mammalian_80S , 7o7y and chain Au create eS24_S24__mammalian_80S , 7o7y and chain Ax create eS25_S25__mammalian_80S , 7o7y and chain Ay create eS26_S26__mammalian_80S , 7o7y and chain AE create eS27_S27__mammalian_80S , 7o7y and chain AA create eS28_S28__mammalian_80S , 7o7y and chain AB create eS30_S30__mammalian_80S , 7o7y and chain AD create eS31_S27A_mammalian_80S , 7o7y and chain AC create eS32_canonical_L41__mammalian_80S , 7o7y and chain Az create RACK1_____mammalian_80S , 7o7y and chain AF create 18S__rRNA_mammalian_80S , 7o7y and chain A2 create SARS-CoV-2_mRNA , 7o7y and chain AH create E-site_tRNA_mammalian_80S , 7o7y and chain AI create P-site_tRNA_mammalian_80S , 7o7y and chain AT ### small cofactors ### create Zn_mammalian_80S , 7o7y and resn ZN create Mg_mammalian_80S , 7o7y and resn MG create water_mammalian_80S , 7o7y and resn HOH create unassigned_ions_mammalian_80S , 7o7y and resn UNX # subselections for the 80S # select proteins , eL* or uL* or eS* or uS* or RACK1 select additional , *tRNA* or *mRNA* or *SARS* 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)) ################## # COLOR SETTINGS # ################## color grey60 , rRNAs color white , bases color aquamarine, uL* or uS* color oxygen , eL6_* or eL22_* or eL27_* or eL28_* or eL29_* or eL36_* color oxygen , eS7_* or eS10_* or eS12_* or eS21_* or eS26_* or RACK1 color orange , eL* and not (eL6_* or eL22_* or eL27_* or eL28_* or eL29_* or eL36_*) color orange , eS* and not (eS7_* or eS10_* or eS12_* or eS21_* or eS26_*) color density , additional util.cnc Zn_mammalian_80S util.cnc Mg_mammalian_80S util.cnc water_mammalian_80S color sand ,unassigned_ions_mammalian_80S hide everything #################### # DISPLAY SETTINGS # #################### show cartoon, proteins or rRNAs or additional set cartoon_loop_radius, 0.4 set cartoon_tube_radius, 0.8 set cartoon_ladder_radius, 0.4 set cartoon_oval_length, 1.2 set cartoon_oval_width, 0.4 show spheres, Zn_mammalian_80S or Mg_mammalian_80S or water_mammalian_80S or unassigned_ions_mammalian_80S set sphere_scale=0.5 delete proteins delete rRNAs delete bases delete additional delete 7o7y ################# # VIEW SETTINGS # ################# # side view of the 80S # ###### set_view (\ -0.987847030, 0.021754943, 0.153153449,\ 0.034389943, -0.934180319, 0.354742438,\ 0.150809333, 0.355729073, 0.922201931,\ 0.031253785, -0.026235104, -856.990112305,\ 178.866989136, 16.027549744, 225.610427856,\ 723.269958496, 987.251403809, -20.000000000 ) ###### ##################################################