5O60

Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.

Hentschel, J.Burnside, C.Mignot, I.Leibundgut, M.Boehringer, D.Ban, N.

(2017) Cell Rep 20: 149-160

  • DOI: 10.1016/j.celrep.2017.06.029
  • Primary Citation of Related Structures:  
    5O61, 5O60, 5O5J

  • PubMed Abstract: 
  • The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance ...

    The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL37A [auth 3]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1916
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10J [auth I]175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplJMSMEG_1364MSMEI_1325
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11K [auth J]142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplKMSMEG_1346MSMEI_1308
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13L [auth K]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14M [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15N [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplOMSMEG_1474
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16O [auth N]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
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Entity ID: 16
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50S ribosomal protein L17P [auth O]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
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Entity ID: 17
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50S ribosomal protein L18Q [auth P]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplRMSMEG_1471
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19R [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
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Entity ID: 19
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50S ribosomal protein L20S [auth R]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
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Entity ID: 20
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50S ribosomal protein L21T [auth S]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
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Entity ID: 21
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50S ribosomal protein L22U [auth T]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
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Entity ID: 22
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50S ribosomal protein L23V [auth U]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
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Entity ID: 23
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50S ribosomal protein L24W [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
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Entity ID: 24
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50S ribosomal protein L25X [auth W]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEG_5431
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Entity ID: 25
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50S ribosomal protein L27Y [auth X]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
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Entity ID: 26
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50S ribosomal protein L28Z [auth Y]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmBMSMEG_2400
UniProt
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Entity ID: 27
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50S ribosomal protein L29AA [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
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Entity ID: 28
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50S ribosomal protein L30BA [auth a]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
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Entity ID: 29
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50S ribosomal protein L32CA [auth b]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmFMSMEG_5489MSMEI_5337
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Entity ID: 30
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50S ribosomal protein L33 1DA [auth c]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmG1rpmG2MSMEG_1339MSMEI_1301
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Entity ID: 31
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50S ribosomal protein L34EA [auth d]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmHMSMEG_6946MSMEI_6752
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Entity ID: 32
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50S ribosomal protein L35FA [auth e]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth f]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmJMSMEG_1520MSMEI_1484
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31HA [auth g]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_4951MSMEI_4823
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Entity ID: 2
MoleculeChainsLengthOrganismImage
23S rRNAB [auth A]3120Mycolicibacterium smegmatis MC2 155
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Entity ID: 3
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5S rRNAC [auth B]118Mycolicibacterium smegmatis MC2 155
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  • Entity ID: 35
    MoleculeChainsLengthOrganismImage
    tRNA CCA-end acetylated (Phe)IA [auth 2]3Mycolicibacterium smegmatis MC2 155
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    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PHE
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    FQ [auth 2]PHENYLALANINE
    C9 H11 N O2
    COLNVLDHVKWLRT-QMMMGPOBSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    AQ [auth c], CQ [auth f], DQ [auth g], ZP [auth Y]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth A] , AI [auth A] , 
    AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  AG [auth A],  AH [auth A],  AI [auth A],  AJ [auth A],  AK [auth A],  AL [auth A],  AM [auth A],  AN [auth A],  AO [auth A],  AP [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  BI [auth A],  BJ [auth A],  BK [auth A],  BL [auth A],  BM [auth A],  BN [auth A],  BO [auth A],  BP [auth A],  BQ [auth c],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth A],  CI [auth A],  CJ [auth A],  CK [auth A],  CL [auth A],  CM [auth A],  CN [auth A],  CO [auth A],  CP [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  DH [auth A],  DI [auth A],  DJ [auth A],  DK [auth A],  DL [auth A],  DM [auth A],  DN [auth A],  DO [auth A],  DP [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth A],  EI [auth A],  EJ [auth A],  EK [auth A],  EL [auth A],  EM [auth A],  EN [auth A],  EO [auth A],  EP [auth A],  EQ [auth 2],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth A],  FI [auth A],  FJ [auth A],  FK [auth A],  FL [auth A],  FM [auth A],  FN [auth A],  FO [auth A],  FP [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth A],  GI [auth A],  GJ [auth A],  GK [auth A],  GL [auth A],  GM [auth A],  GN [auth A],  GO [auth A],  GP [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth A],  HI [auth A],  HJ [auth A],  HK [auth A],  HL [auth A],  HM [auth A],  HN [auth A],  HO [auth A],  HP [auth B],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth A],  II [auth A],  IJ [auth A],  IK [auth A],  IL [auth A],  IM [auth A],  IN [auth A],  IO [auth A],  IP [auth B],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  JH [auth A],  JI [auth A],  JJ [auth A],  JK [auth A],  JL [auth A],  JM [auth A],  JN [auth A],  JO [auth A],  JP [auth B],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  KH [auth A],  KI [auth A],  KJ [auth A],  KK [auth A],  KL [auth A],  KM [auth A],  KN [auth A],  KO [auth A],  KP [auth B],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth A],  LI [auth A],  LJ [auth A],  LK [auth A],  LL [auth A],  LM [auth A],  LN [auth A],  LO [auth A],  LP [auth B],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  MH [auth A],  MI [auth A],  MJ [auth A],  MK [auth A],  ML [auth A],  MM [auth A],  MN [auth A],  MO [auth A],  MP [auth B],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  NG [auth A],  NH [auth A],  NI [auth A],  NJ [auth A],  NK [auth A],  NL [auth A],  NM [auth A],  NN [auth A],  NO [auth A],  NP [auth B],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  OG [auth A],  OH [auth A],  OI [auth A],  OJ [auth A],  OK [auth A],  OL [auth A],  OM [auth A],  ON [auth A],  OO [auth A],  OP [auth B],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  PG [auth A],  PH [auth A],  PI [auth A],  PJ [auth A],  PK [auth A],  PL [auth A],  PM [auth A],  PN [auth A],  PO [auth A],  PP [auth B],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth A],  QH [auth A],  QI [auth A],  QJ [auth A],  QK [auth A],  QL [auth A],  QM [auth A],  QN [auth A],  QO [auth A],  QP [auth C],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth A],  RH [auth A],  RI [auth A],  RJ [auth A],  RK [auth A],  RL [auth A],  RM [auth A],  RN [auth A],  RO [auth A],  RP [auth C],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth A],  SH [auth A],  SI [auth A],  SJ [auth A],  SK [auth A],  SL [auth A],  SM [auth A],  SN [auth A],  SO [auth A],  SP [auth C],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth A],  TH [auth A],  TI [auth A],  TJ [auth A],  TK [auth A],  TL [auth A],  TM [auth A],  TN [auth A],  TO [auth A],  TP [auth C],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth A],  UH [auth A],  UI [auth A],  UJ [auth A],  UK [auth A],  UL [auth A],  UM [auth A],  UN [auth A],  UO [auth A],  UP [auth D],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  VF [auth A],  VG [auth A],  VH [auth A],  VI [auth A],  VJ [auth A],  VK [auth A],  VL [auth A],  VM [auth A],  VN [auth A],  VO [auth A],  VP [auth F],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  WF [auth A],  WG [auth A],  WH [auth A],  WI [auth A],  WJ [auth A],  WK [auth A],  WL [auth A],  WM [auth A],  WN [auth A],  WO [auth A],  WP [auth N],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  XF [auth A],  XG [auth A],  XH [auth A],  XI [auth A],  XJ [auth A],  XK [auth A],  XL [auth A],  XM [auth A],  XN [auth A],  XO [auth A],  XP [auth N],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  YF [auth A],  YG [auth A],  YH [auth A],  YI [auth A],  YJ [auth A],  YK [auth A],  YL [auth A],  YM [auth A],  YN [auth A],  YO [auth A],  YP [auth T],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZF [auth A],  ZG [auth A],  ZH [auth A],  ZI [auth A],  ZJ [auth A],  ZK [auth A],  ZL [auth A],  ZM [auth A],  ZN [auth A],  ZO [auth A]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.18 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Swiss National Science FoundationSwitzerland310030B_163478
    NCCR RNA and disease program, SNSFSwitzerland51NF40_141735

    Revision History  (Full details and data files)

    • Version 1.0: 2017-07-12
      Type: Initial release
    • Version 1.1: 2017-07-19
      Changes: Database references
    • Version 1.2: 2018-10-17
      Changes: Data collection, Refinement description
    • Version 1.3: 2019-12-11
      Changes: Other