# ###################################################################################### # PyMOL script for display of the tobacco (Nicotiana tabacum) 80S cytosolic 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: 04/04/2024 # # 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: # # Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. # Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R. # Nat Plants 9:987-1000 (2023) # # 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) # # An updated nomenclature for plant ribosomal protein genes. # Scarpin MR, Busche M, Martinez RE, Harper LC, Reiser L, Szakonyi D, Merchante C, Lan T, Xiong W, Mo B, Tang G, Chen X, # Bailey-Serres J, Browning KS, Brunkard JO. # The Plant Cell 35(2):640-643 (2023) # # Abbreviations: # uS../uL.. universally conserved proteins (eukaryotes, archaea and bacteria) # eS../eL.. archaeal- and eukaryotic-specific proteins # # Color Scheme: # light blue: proteins universally conserved # orange: proteins conserved in archaea and eukaryotes # red: proteins eukaryotic-specific # dark blue: mRNA, tRNAs, nascent chain # light grey: rRNAs # chemical standard: ions and ligands # ################ # INSTRUCTIONS # ################ # # 1) Start PyMOL # The structure of the 80S plant ribosome has been deposited at the PDB in mmCIF format. Only more 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 8b2l # # 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 plant cytosolic 80s ribosome (8b2l) # onto the large subunit of the yeast 80S ribosome (PDB ID 4v88, molecule B in the asymmetric subunit) cmd.transform_selection("8b2l", [0.5427879095077515, -0.7174276113510132, -0.43666791915893555, 287.8698347522786, 0.839840829372406, 0.4679601192474365, 0.27510127425193787, -301.49062907315056, 0.006977916229516268, -0.5160531997680664, 0.856528103351593, 163.1387338892883, 0.0, 0.0, 0.0, 1.0],homogenous=1) ############## # SELECTIONS # ############## ### small 40S subunit ############################# create uS2__SA___plant_80S , 8b2l and chain Z1 create uS3__S3___plant_80S , 8b2l and chain a1 create uS4__S9___plant_80S , 8b2l and chain b1 create uS5__S2___plant_80S , 8b2l and chain c1 create uS7__S5___plant_80S , 8b2l and chain d1 create uS8__S15A_plant_80S , 8b2l and chain e1 create uS9__S16__plant_80S , 8b2l and chain f1 create uS10_S20__plant_80S , 8b2l and chain R1 create uS11_S14__plant_80S , 8b2l and chain S1 create uS12_S23__plant_80S , 8b2l and chain T1 create uS13_S18__plant_80S , 8b2l and chain U1 create uS14_S29__plant_80S , 8b2l and chain V1 create uS15_S13__plant_80S , 8b2l and chain W1 create uS17_S11__plant_80S , 8b2l and chain X1 create uS19_S15__plant_80S , 8b2l and chain Y1 create eS1__S3A__plant_80S , 8b2l and chain F1 create eS4__S4___plant_80S , 8b2l and chain A1 create eS6__S6___plant_80S , 8b2l and chain k1 create eS7__S7___plant_80S , 8b2l and chain O1 create eS8__S8___plant_80S , 8b2l and chain P1 create eS10_S10__plant_80S , 8b2l and chain l1 create eS12_S12__plant_80S , 8b2l and chain C1 create eS17_S17__plant_80S , 8b2l and chain D1 create eS19_S19__plant_80S , 8b2l and chain E1 create eS21_S21__plant_80S , 8b2l and chain G1 create eS24_S24__plant_80S , 8b2l and chain H1 create eS25_S25__plant_80S , 8b2l and chain I1 create eS26_S26__plant_80S , 8b2l and chain J1 create eS27_S27__plant_80S , 8b2l and chain K1 create eS28_S28__plant_80S , 8b2l and chain L1 create eS30_S30__plant_80S , 8b2l and chain M1 create eS31_S27A_plant_80S , 8b2l and chain N1 create eS32_canonical_L41_plant_80S, 8b2l and chain p3 create RACK1_RACK1_plant_80S , 8b2l and chain Q1 create 18S_rRNA____plant_80S , 8b2l and chain h1 create mRNA________plant_80S , 8b2l and chain B1 create P-site_tRNA_plant_80S , 8b2l and chain i2 create E-site_tRNA_plant_80S , 8b2l and chain W2 # large 60S subunit ############################ create eL6__L6___plant_80S , 8b2l and chain b3 create eL8__L7A__plant_80S , 8b2l and chain c3 create eL13_L13__plant_80S , 8b2l and chain D3 create eL14_L14__plant_80S , 8b2l and chain E3 create eL15_L15__plant_80S , 8b2l and chain F3 create eL18_L18__plant_80S , 8b2l and chain G3 create eL19_L19__plant_80S , 8b2l and chain H3 create eL20_L18A_plant_80S , 8b2l and chain I3 create eL21_L21__plant_80S , 8b2l and chain J3 create eL22_L22__plant_80S , 8b2l and chain K3 create eL24_L24__plant_80S , 8b2l and chain L3 create eL27_L27__plant_80S , 8b2l and chain M3 create eL28_L28__plant_80S , 8b2l and chain N3 create eL29_L29__plant_80S , 8b2l and chain O3 create eL30_L30__plant_80S , 8b2l and chain P3 create eL31_L31__plant_80S , 8b2l and chain Q3 create eL32_L32__plant_80S , 8b2l and chain R3 create eL33_L35A_plant_80S , 8b2l and chain S3 create eL34_L34__plant_80S , 8b2l and chain T3 create eL36_L36__plant_80S , 8b2l and chain U3 create eL37_L37__plant_80S , 8b2l and chain V3 create eL38_L38__plant_80S , 8b2l and chain W3 create eL39_L39__plant_80S , 8b2l and chain X3 create eL40_L40__plant_80S , 8b2l and chain Y3 create eL42_L44__plant_80S , 8b2l and chain Z3 create eL43_L37A_plant_80S , 8b2l and chain a3 create uL2__L8___plant_80S , 8b2l and chain o3 create uL3_L3____plant_80S , 8b2l and chain r3 create uL4_L4____plant_80S , 8b2l and chain s3 create uL5_L11___plant_80S , 8b2l and chain t3 create uL6_L9____plant_80S , 8b2l and chain u3 create uL13_L13A_plant_80S , 8b2l and chain d3 create uL14_L23__plant_80S , 8b2l and chain e3 create uL15_L27A_plant_80S , 8b2l and chain f3 create uL16_L10__plant_80S , 8b2l and chain g3 create uL18_L5___plant_80S , 8b2l and chain h3 create uL22_L17__plant_80S , 8b2l and chain j3 create uL23_L23A_plant_80S , 8b2l and chain k3 create uL24_L26__plant_80S , 8b2l and chain m3 create uL29_L35__plant_80S , 8b2l and chain n3 create uL30_L7___plant_80S , 8b2l and chain q3 create NC________plant_80S , 8b2l and chain l3 create 25S_rRNA__plant_80S , 8b2l and chain A3 create 5.8S_rRNA_plant_80S , 8b2l and chain B3 create 5S_rRNA___plant_80S , 8b2l and chain C3 ### ligands ### create Mg_________plant_80S , 8b2l and resn MG create Zn_________plant_80S , 8b2l and resn ZN create K__________plant_80S , 8b2l and resn K create other_cofactors_plant_80S , 8b2l and (resn SPM or resn SPD) ################## # COLOR SETTINGS # ################## ### temporary subselections for the 80S ### select proteins, eL* or uL* or eS* or uS* or RACK1* select additional, *tRNA* or NC_* 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 grey60, rRNAs color white, bases color aquamarine, uS* or uL* 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 Mg_* or Zn_* or K_* color white, other_cofactors_plant_80S util.cnc other_cofactors_plant_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, Mg_* or Zn_* or K_* set sphere_scale=0.5 show sticks, other_cofactors_plant_80S delete proteins delete rRNAs delete bases delete additional delete 8b2l ################# # 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,\ 0.000000000, 0.000000000, -855.260559082,\ 179.838546753, 3.613739014, 232.099822998,\ 723.269958496, 987.251403809, -20.000000000 ) ####### ##################################################