# ################################################################## # PyMOL script for display of the Escherichia coli 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: 03/28/2024 # # 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: # # High-resolution structure of the Escherichia coli ribosome. # Noeske J, Wasserman MR, Terry DS, Altman RB, Blanchard SC, Cate JH. # Nat Struct Mol Biol. 22(4):336-41. (2015) # # 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) # bS../bL.. bacterial-specific proteins # # Color Scheme: # light blue: proteins universally conserved # magenta: proteins bacterial-specific # light grey: rRNA # green spheres: magnesium ions # red spheres: water # grey spheres: Zn ions # white sticks: other cofactors # ######################################### # INSTRUCTIONS FOR RUNNING THIS SCRIPT # ######################################### # # 1) Start PyMOL # The structure of the 70S E. coli 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 4ybb # # 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 # ######################## ### temporary selection for one 70S in the ASU ### create 4ybb_molAD, 4ybb and (chain A* or chain D*) delete 4ybb # the following matrix superimposes the 70S bacterial ribosome from E. coli (4ybb_molAD) # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the asymmetric unit) cmd.transform_selection("4ybb_molAD", [-0.038011737167835236, 0.9714407920837402, -0.23421764373779297, 199.98798171097008, 0.6521817445755005, -0.15346747636795044, -0.7423655986785889, 52.4952423891134, -0.7571090459823608, -0.18097107112407684, -0.6277223825454712, 166.73911404074198, 0.0, 0.0, 0.0, 1.0],homogenous=1) ################################# # SELECTIONS OF PROTEIN AND RNA # ################################# ### 30S bacterial small subunit ### create uS2__S2__bacterial_70S , 4ybb_molAD and chain AB create uS3__S3__bacterial_70S , 4ybb_molAD and chain AC create uS4__S4__bacterial_70S , 4ybb_molAD and chain AD create uS5__S5__bacterial_70S , 4ybb_molAD and chain AE create bS6__S6__bacterial_70S , 4ybb_molAD and chain AF create uS7__S7__bacterial_70S , 4ybb_molAD and chain AG create uS8__S8__bacterial_70S , 4ybb_molAD and chain AH create uS9__S9__bacterial_70S , 4ybb_molAD and chain AI create uS10_S10_bacterial_70S , 4ybb_molAD and chain AJ create uS11_S11_bacterial_70S , 4ybb_molAD and chain AK create uS12_S12_bacterial_70S , 4ybb_molAD and chain AL create uS13_S13_bacterial_70S , 4ybb_molAD and chain AM create uS14_S14_bacterial_70S , 4ybb_molAD and chain AN create uS15_S15_bacterial_70S , 4ybb_molAD and chain AO create bS16_S16_bacterial_70S , 4ybb_molAD and chain AP create uS17_S17_bacterial_70S , 4ybb_molAD and chain AQ create bS18_S18_bacterial_70S , 4ybb_molAD and chain AR create uS19_S19_bacterial_70S , 4ybb_molAD and chain AS create bS20_S20_bacterial_70S , 4ybb_molAD and chain AT create bS21_S21_bacterial_70S , 4ybb_molAD and chain AU create 16S_rRNA_bacterial_70S , 4ybb_molAD and chain AA ### 50S bacterial large subunit ### create uL2__L2__bacterial_70S , 4ybb_molAD and chain DC create uL3__L3__bacterial_70S , 4ybb_molAD and chain DD create uL4__L4__bacterial_70S , 4ybb_molAD and chain DE create uL5__L5__bacterial_70S , 4ybb_molAD and chain DF create uL6__L6__bacterial_70S , 4ybb_molAD and chain DG create bL9__L9__bacterial_70S , 4ybb_molAD and chain DH create uL10_L10_bacterial_70S , 4ybb_molAD and chain DI create uL11_L11_bacterial_70S , 4ybb_molAD and chain DJ create uL13_L13_bacterial_70S , 4ybb_molAD and chain DK create uL14_L14_bacterial_70S , 4ybb_molAD and chain DL create uL15_L15_bacterial_70S , 4ybb_molAD and chain DM create uL16_L16_bacterial_70S , 4ybb_molAD and chain DN create bL17_L17_bacterial_70S , 4ybb_molAD and chain DO create uL18_L18_bacterial_70S , 4ybb_molAD and chain DP create bL19_L19_bacterial_70S , 4ybb_molAD and chain DQ create bL20_L20_bacterial_70S , 4ybb_molAD and chain DR create bL21_L21_bacterial_70S , 4ybb_molAD and chain DS create uL22_L22_bacterial_70S , 4ybb_molAD and chain DT create uL23_L23_bacterial_70S , 4ybb_molAD and chain DU create uL24_L24_bacterial_70S , 4ybb_molAD and chain DV create bL25_L25_bacterial_70S , 4ybb_molAD and chain DW create bL27_L27_bacterial_70S , 4ybb_molAD and chain DX create bL28_L28_bacterial_70S , 4ybb_molAD and chain DY create uL29_L29_bacterial_70S , 4ybb_molAD and chain DZ create uL30_L30_bacterial_70S , 4ybb_molAD and chain D0 create bL32_L32_bacterial_70S , 4ybb_molAD and chain D1 create bL33_L33_bacterial_70S , 4ybb_molAD and chain D2 create bL34_L34_bacterial_70S , 4ybb_molAD and chain D3 create bL35_L35_bacterial_70S , 4ybb_molAD and chain D4 create bL36_L36_bacterial_70S , 4ybb_molAD and chain D5 create 23S_rRNA_bacterial_70S , 4ybb_molAD and chain DA create 5S__rRNA_bacterial_70S , 4ybb_molAD and chain DB ### 70S cofactors ### create Mg__bacterial_70S , 4ybb_molAD and resn MG create HOH_bacterial_70S , 4ybb_molAD and resn HOH create Zn__bacterial_70S , 4ybb_molAD and resn ZN create other_cofactors_bacterial_70S , 4ybb_molAD and (resn 1PE or resn ACY or resn EDO or resn GUN or resn MPD or resn PEG or resn PG4 or resn PGE or resn PUT or resn SPD or resn TRS) ### temporary subselections for coloring and display ### select proteins_bacterial_70S, bL* or uL* or bS* or uS* select rRNAs_bacterial_70S, *rRNA* select bases_bacterial_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 SETTINGS # ################## color grey60, rRNAs_bacterial_70S color white, bases_bacterial_70S color aquamarine, uL* or uS* color violet, bL* or bS* util.cnc Mg__bacterial_70S util.cnc HOH_bacterial_70S util.cnc Zn__bacterial_70S color white, other_cofactors_bacterial_70S util.cnc other_cofactors_bacterial_70S hide everything #################### # DISPLAY SETTINGS # #################### show cartoon, proteins_bacterial_70S show cartoon, rRNAs_bacterial_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__bacterial_70S show spheres, Mg__bacterial_70S show spheres, HOH_bacterial_70S show sticks, other_cofactors_bacterial_70S set sphere_scale=0.5 set stick_radius=0.2 delete proteins_bacterial_70S delete rRNAs_bacterial_70S delete bases_bacterial_70S delete 4ybb_molAD ################# # VIEW SETTINGS # ################# ### side view of the 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 ) ######