# #################################################################################### # PyMOL script for display of the Thermococcus kodakarensis archaeal 70S ribosome # #################################################################################### # # 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 # http://www.bangroup.ethz.ch/research/nomenclature-of-ribosomal-proteins.html # # Citation for structure: # # Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. # Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, # Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, # Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, # Shalev-Benami M, Meier JL, Schwartz S. # Nature 583: 638-643 (2020) # # 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 # aS../aL.. archaeal-specific proteins # # Color Scheme: # blue: proteins universally conserved # orange: proteins conserved in archaea and eukaryotes # olive: proteins archaeal-specific or found at 2nd position # dark blue: associated SBDS factor # white: unassigned protein segment # light grey: rRNA # red spheres: water # grey spheres: Zn ions # ######################################### # INSTRUCTIONS FOR RUNNING THIS SCRIPT # ######################################### # # 1) Start PyMOL # The structure of the 70S T. kodakarensis 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 v2.2.5 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 6skg # # 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 # ######################## # the following matrix superimposes the 70S archaeal ribosome from T. kodakarensis (6skg) # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the asymmetric unit) cmd.transform_selection("6skg", [-0.26694244146347046, 0.8728165626525879, 0.4085743725299835, -27.052292722303264, 0.28448671102523804, -0.33369675278663635, 0.8987289667129517, -173.2293806879452, 0.9207654595375061, 0.35614287853240967, -0.1592268943786621, 6.476521529159982, 0.0, 0.0, 0.0, 1.0],homogenous=1) ### 30S archaeal small subunit ### create eS1__S3Ae_____archaeal_70S , 6skg and chain Ad create uS2__S2_______archaeal_70S , 6skg and chain Ab create uS3__S3_______archaeal_70S , 6skg and chain Ac create uS4__S4_______archaeal_70S , 6skg and chain Ae create eS4__S4e______archaeal_70S , 6skg and chain Af create uS5__S5_______archaeal_70S , 6skg and chain Ag create eS6__S6e______archaeal_70S , 6skg and chain Ah create uS7__S7_______archaeal_70S , 6skg and chain Ai create uS8__S8_______archaeal_70S , 6skg and chain Aj create eS8__S8e______archaeal_70S , 6skg and chain Ak create uS9__S9_______archaeal_70S , 6skg and chain Al create uS10_S10______archaeal_70S , 6skg and chain Am create uS11_S11______archaeal_70S , 6skg and chain An create uS12_S12______archaeal_70S , 6skg and chain Ao create uS13_S13______archaeal_70S , 6skg and chain Ap create uS15_S15______archaeal_70S , 6skg and chain Aq create uS14_S14______archaeal_70S , 6skg and chain Ar create uS17_S17______archaeal_70S , 6skg and chain As create eS17_S17e_____archaeal_70S , 6skg and chain At create uS19_S19______archaeal_70S , 6skg and chain Au create eS19_S19e_____archaeal_70S , 6skg and chain Av create aSnew_at_eS21_position , 6skg and chain Az create eS24_S24e_____archaeal_70S , 6skg and chain Aw create eS27_S27e_____archaeal_70S , 6skg and chain Ax create eS28_S28e_____archaeal_70S , 6skg and chain Ay create eS32_L41e_____archaeal_70S , 6skg and chain Bk create 16S__rRNA_____archaeal_70S , 6skg and chain Aa ### 50S archaeal large subunit ### create uL2__L2_______archaeal_70S , 6skg and chain BC create uL3__L3_______archaeal_70S , 6skg and chain BD create uL4__L4_______archaeal_70S , 6skg and chain BE create uL5__L5_______archaeal_70S , 6skg and chain BF create uL6__L6_______archaeal_70S , 6skg and chain BG create eL8__L7Ae_____archaeal_70S , 6skg and chain BH create eL8__L7Ae_at_2nd_position , 6skg and chain BI create uL13_L13______archaeal_70S , 6skg and chain BK create uL14_L14______archaeal_70S , 6skg and chain BL create eL14_L14e_____archaeal_70S , 6skg and chain BN create eL14_L14e_at_eL27_position , 6skg and chain BM create uL15_L15______archaeal_70S , 6skg and chain BO create eL15_L15e_____archaeal_70S , 6skg and chain BP create uL16_L16______archaeal_70S , 6skg and chain BJ create uL18_L18______archaeal_70S , 6skg and chain BQ create eL18_L18e_____archaeal_70S , 6skg and chain BR create eL19_L19e_____archaeal_70S , 6skg and chain BS create eL20_L18Ae_LX_archaeal_70S , 6skg and chain BT create eL21_L21e_____archaeal_70S , 6skg and chain BU create uL22_L22______archaeal_70S , 6skg and chain BV create uL23_L23______archaeal_70S , 6skg and chain BW create uL24_L24______archaeal_70S , 6skg and chain BX create eL24_L24e_____archaeal_70S , 6skg and chain BY create uL29_L29______archaeal_70S , 6skg and chain BZ create uL30_L30______archaeal_70S , 6skg and chain Ba create eL30_L30e_____archaeal_70S , 6skg and chain Bb create eL31_L31e_____archaeal_70S , 6skg and chain Bc create eL32_L32e_____archaeal_70S , 6skg and chain Bd create eL33_L35Ae____archaeal_70S , 6skg and chain Bf create eL34_L34e_____archaeal_70S , 6skg and chain Be create eL43_L37Ae____archaeal_70S , 6skg and chain Bg create eL37_L37e_____archaeal_70S , 6skg and chain Bh create eL39_L39e_____archaeal_70S , 6skg and chain Bi create eL40_L40e_____archaeal_70S , 6skg and chain Bj create eL42_L44e_____archaeal_70S , 6skg and chain Bl create 23S__rRNA_____archaeal_70S , 6skg and chain BA create 5S___rRNA_____archaeal_70S , 6skg and chain BB create eS17_S17e_at_2nd_LSU_position, 6skg and chain Bm create eS24_S24e_at_2nd_LSU_position, 6skg and chain Bn create aLnew_C2H2-type_ZNF_in_LSU , 6skg and chain Bo create archaeal_SBDS , 6skg and chain Bp create unassigned_LSU_protein , 6skg and chain Bq ### 70S cofactors ### create HOH_archaeal_70S , 6skg and resn HOH create Zn__archaeal_70S , 6skg and resn ZN ### temporary subselections for coloring and display ### select proteins_archaeal_70S, eL* or uL* or eS* or uS* or archaeal_SBDS or *position* or unassigned_LSU_protein or aLnew_C2H2-type_ZNF_in_LSU select rRNAs_archaeal_70S , *rRNA* select bases_archaeal_70S , (*RNA* 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 grey60, rRNAs_archaeal_70S color white, bases_archaeal_70S color aquamarine, uL* or uS* color orange, eL* or eS* color deepolive, aLnew_C2H2-type_ZNF_in_LSU or *position* color density, archaeal_SBDS color white, unassigned_LSU_protein util.cnc HOH_archaeal_70S util.cnc Zn__archaeal_70S hide everything #################### # DISPLAY SETTINGS # #################### show cartoon, proteins_archaeal_70S show cartoon, rRNAs_archaeal_70S 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__archaeal_70S show spheres, HOH_archaeal_70S set sphere_scale=0.5 delete proteins_archaeal_70S delete rRNAs_archaeal_70S delete bases_archaeal_70S delete 6skg ################# # VIEW SETTINGS # ################# ### side view of the archaeal 70S ### set_view (\ -0.987847030, 0.021754943, 0.153153449,\ 0.034389943, -0.934180319, 0.354742438,\ 0.150809333, 0.355729073, 0.922201931,\ 0.000000000, 0.000000000, -855.260559082,\ 179.838546753, 3.613739014, 232.099822998,\ 723.269958496, 987.251403809, -20.000000000 ) ######