################################################################################## # PyMOL script for display of the 80S ribosome of baker's yeast (S. cerevisiae) # ################################################################################## # # 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: 03/25/2024 # # 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 eukaryotic ribosome at 3.0 Å resolution. # Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. # Science. 334(6062):1524-9. (2011) # # 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../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: Stm1 stalling factor # light grey: rRNA # green spheres: magnesium ions # grey spheres: Zn ions # blue spheres: hexacoordinated osmium ions (Os*6NH3) # ######################################### # INSTRUCTIONS FOR RUNNING THIS SCRIPT # ######################################### # # 1) Start PyMOL # The structure of the S. cerevisiae 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 4v88 # # 3) Wait until the file is loaded and you can see the 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 # ######################## # temporary subselections # create 4v88_molB, 4v88 and (chain C* or chain D* or chain A5 or chain A6 chain A7 or chain A8) delete 4v88 ################################# # SELECTIONS OF PROTEIN and RNA # ################################# ### 60S proteins and rRNAs ### create uL2__L2___fungal_80S , 4v88_molB and chain DA create uL3__L3___fungal_80S , 4v88_molB and chain DB create uL4__L4___fungal_80S , 4v88_molB and chain DC create uL5__L11__fungal_80S , 4v88_molB and chain DJ create uL6__L9___fungal_80S , 4v88_molB and chain DH create eL6__L6___fungal_80S , 4v88_molB and chain DE create eL8__L8___fungal_80S , 4v88_molB and chain DG create uL10_P0___fungal_80S , 4v88_molB and chain Dq create uL11_L12__fungal_80S , 4v88_molB and chain DK create uL13_L16__fungal_80S , 4v88_molB and chain DO create eL13_L13__fungal_80S , 4v88_molB and chain DL create uL14_L23__fungal_80S , 4v88_molB and chain DV create eL14_L14__fungal_80S , 4v88_molB and chain DM create uL15_L28__fungal_80S , 4v88_molB and chain Da create eL15_L15__fungal_80S , 4v88_molB and chain DN create uL16_L10__fungal_80S , 4v88_molB and chain DI create uL18_L5___fungal_80S , 4v88_molB and chain DD create eL18_L18__fungal_80S , 4v88_molB and chain DQ create eL19_L19__fungal_80S , 4v88_molB and chain DR create eL20_L20__fungal_80S , 4v88_molB and chain DS create eL21_L21__fungal_80S , 4v88_molB and chain DT create uL22_L17__fungal_80S , 4v88_molB and chain DP create eL22_L22__fungal_80S , 4v88_molB and chain DU create uL23_L25__fungal_80S , 4v88_molB and chain DX create uL24_L26__fungal_80S , 4v88_molB and chain DY create eL24_L24__fungal_80S , 4v88_molB and chain DW create eL27_L27__fungal_80S , 4v88_molB and chain DZ create uL29_L35__fungal_80S , 4v88_molB and chain Dh create eL29_L29__fungal_80S , 4v88_molB and chain Db create uL30_L7___fungal_80S , 4v88_molB and chain DF create eL30_L30__fungal_80S , 4v88_molB and chain Dc create eL31_L31__fungal_80S , 4v88_molB and chain Dd create eL32_L32__fungal_80S , 4v88_molB and chain De create eL33_L33__fungal_80S , 4v88_molB and chain Df create eL34_L34__fungal_80S , 4v88_molB and chain Dg create eL36_L36__fungal_80S , 4v88_molB and chain Di create eL37_L37__fungal_80S , 4v88_molB and chain Dj create eL38_L38__fungal_80S , 4v88_molB and chain Dk create eL39_L39__fungal_80S , 4v88_molB and chain Dl create eL40_L40__fungal_80S , 4v88_molB and chain Dm ### note: the non-canonical eS32 (previously named eL41) is not present in the crystal strucutre create eL40_L40__fungal_80S , 4v88_molB and chain Dm create eL42_L42__fungal_80S , 4v88_molB and chain Do create eL43_L43__fungal_80S , 4v88_molB and chain Dp create P1________fungal_80S , 4v88_molB and chain Dr create P2________fungal_80S , 4v88_molB and chain Ds create 25S__rRNA_fungal_80S , 4v88_molB and chain A5 create 5S___rRNA_fungal_80S , 4v88_molB and chain A7 create 5.8S_rRNA_fungal_80S , 4v88_molB and chain A8 ### 40S proteins, rRNA and bound Stm1 ### create eS1__S1___fungal_80S , 4v88_molB and chain CB create uS2__S0___fungal_80S , 4v88_molB and chain CA create uS3__S3___fungal_80S , 4v88_molB and chain CD create uS4__S9___fungal_80S , 4v88_molB and chain CJ create eS4__S4___fungal_80S , 4v88_molB and chain CE create uS5__S2___fungal_80S , 4v88_molB and chain CC create eS6__S6___fungal_80S , 4v88_molB and chain CG create uS7__S5___fungal_80S , 4v88_molB and chain CF create eS7__S7___fungal_80S , 4v88_molB and chain CH create uS8__S22__fungal_80S , 4v88_molB and chain CW create eS8__S8___fungal_80S , 4v88_molB and chain CI create uS9__S16__fungal_80S , 4v88_molB and chain CQ create uS10_S20__fungal_80S , 4v88_molB and chain CU create eS10_S10__fungal_80S , 4v88_molB and chain CK create uS11_S14__fungal_80S , 4v88_molB and chain CO create uS12_S23__fungal_80S , 4v88_molB and chain CX create eS12_S12__fungal_80S , 4v88_molB and chain CM create uS13_S18__fungal_80S , 4v88_molB and chain CS create uS14_S29__fungal_80S , 4v88_molB and chain Cd create uS15_S13__fungal_80S , 4v88_molB and chain CN create uS17_S11__fungal_80S , 4v88_molB and chain CL create eS17_S17__fungal_80S , 4v88_molB and chain CR create uS19_S15__fungal_80S , 4v88_molB and chain CP create eS19_S19__fungal_80S , 4v88_molB and chain CT create eS21_S21__fungal_80S , 4v88_molB and chain CV create eS24_S24__fungal_80S , 4v88_molB and chain CY create eS25_S25__fungal_80S , 4v88_molB and chain CZ create eS26_S26__fungal_80S , 4v88_molB and chain Ca create eS27_S27__fungal_80S , 4v88_molB and chain Cb create eS28_S28__fungal_80S , 4v88_molB and chain Cc create eS30_S30__fungal_80S , 4v88_molB and chain Ce create eS31_S31__fungal_80S , 4v88_molB and chain Cf create eS32_canonical_L41_fungal_80S , 4v88_molB and chain Dn create RACK1_____fungal_80S , 4v88_molB and chain Cg create 18S_rRNA__fungal_80S , 4v88_molB and chain A6 create Stm1 , 4v88_molB and chain Ch ### small cofactors ### create Zn_fungal_80S , 4v88_molB and resn ZN create Mg_fungal_80S , 4v88_molB and resn MG create Os6HN3_fungal_80S , 4v88_molB and resn OHX # subselections for the 80S # select proteins , P1_* or P2_* or eL* or uL* or eS* or uS* or RACK1 select additional , Stm1 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 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 , P1_* or P2_* color orange , eS* and not (eS7_* or eS10_* or eS12_* or eS21_* or eS26_*) color density , additional util.cnc Zn_fungal_80S util.cnc Mg_fungal_80S util.cnc Os6HN3_fungal_80S hide everything #################### # DISPLAY SETTINGS # #################### show cartoon, proteins or rRNAs or additional 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, Zn_fungal_80S or Mg_fungal_80S or Os6HN3_fungal_80S set sphere_scale=0.5 delete proteins delete rRNAs delete bases delete additional delete 4v88_molB ################# # 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 ) ######