5TCU

Methicillin sensitive Staphylococcus aureus 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome.

Belousoff, M.J.Eyal, Z.Radjainia, M.Ahmed, T.Bamert, R.S.Matzov, D.Bashan, A.Zimmerman, E.Mishra, S.Cameron, D.Elmlund, H.Peleg, A.Y.Bhushan, S.Lithgow, T.Yonath, A.

(2017) mBio 8

  • DOI: 10.1128/mBio.00395-17
  • Primary Citation of Related Structures:  
    5T7V, 5TCU

  • PubMed Abstract: 
  • An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center ...

    An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel trevor.lithgow@monash.edu ada.yonath@weizmann.ac.il.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth SB]202Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsCSAOUHSC_02506
UniProt
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth SC]198Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsDSAOUHSC_01829
UniProt
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth SD]156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsESAOUHSC_02494
UniProt
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth SE]95Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsFSAOUHSC_00348
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth SG]155Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsGSAOUHSC_00528
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth SF]130Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsHSAOUHSC_02498
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth SH]127Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsISAOUHSC_02477
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth S1]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth S2]114Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsKSAOUHSC_02486
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth S3]136Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsLSAOUHSC_00527
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth S4]113Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsMSAOUHSC_02487
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZM [auth S5]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsZrpsN1SAOUHSC_02499
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth S6]88Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsOSAOUHSC_01250
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth S7]83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsPSAOUHSC_01208
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth S8]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsQSAOUHSC_02503
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth S9]56Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsRSAOUHSC_00350
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth SI]78Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsSSAOUHSC_02508
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth SA]79Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsTSAOUHSC_01689
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth L2]274Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth LC]215Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth LJ]205Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth LK]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth LL]174Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth LM]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth LN]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth LO]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth LP]136Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
UniProt
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth LQ]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
UniProt
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18IA [auth LR]113Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth L1]109Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
UniProt
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Entity ID: 37
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50S ribosomal protein L20KA [auth L3]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
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Entity ID: 38
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50S ribosomal protein L21LA [auth L4]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22MA [auth L5]112Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth L6]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24OA [auth L7]103Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25PA [auth L8]93Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplYctcSAOUHSC_00474
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Entity ID: 43
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50S ribosomal protein L27QA [auth L9]82Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
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Entity ID: 44
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50S ribosomal protein L28RA [auth LA]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmBSAOUHSC_01191
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Entity ID: 45
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50S ribosomal protein L29SA [auth LB]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
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Entity ID: 46
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50S ribosomal protein L30TA [auth LD]57Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
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Entity ID: 47
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50S ribosomal protein L32UA [auth LE]47Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L33 1VA [auth LS]47Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmG1SAOUHSC_01328
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Entity ID: 49
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50S ribosomal protein L34WA [auth LG]43Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
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Entity ID: 50
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50S ribosomal protein L35XA [auth LH]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
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Entity ID: 51
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50S ribosomal protein L36YA [auth LI]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmJSAOUHSC_02488
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Entity ID: 52
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50S ribosomal protein L31 type BZA [auth LF]74Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmE2SAOUHSC_02361
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAA1555Staphylococcus aureus subsp. aureus NCTC 8325
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  • Entity ID: 20
    MoleculeChainsLengthOrganismImage
    mRNAT [auth X]13Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 21
    MoleculeChainsLengthOrganismImage
    P-site tRNA CHAINU [auth E]75Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 22
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    E-site tRNA CHAINV [auth D]76Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 23
    MoleculeChainsLengthOrganismImage
    23S RRNAW [auth B]2923Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 24
    MoleculeChainsLengthOrganismImage
    5S rRNA CHAINX [auth C]114Staphylococcus aureus subsp. aureus NCTC 8325
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    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PAR (Subject of Investigation/LOI)
    Query on PAR

    Download Ideal Coordinates CCD File 
    AB [auth A]PAROMOMYCIN
    C23 H45 N5 O14
    UOZODPSAJZTQNH-LSWIJEOBSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AC [auth A] , AD [auth B] , AE [auth B] , AF [auth B] , BB [auth A] , BC [auth A] , BD [auth B] , BE [auth B] , 
    AC [auth A], AD [auth B], AE [auth B], AF [auth B], BB [auth A], BC [auth A], BD [auth B], BE [auth B], BF [auth B], CB [auth A], CC [auth SG], CD [auth B], CE [auth B], CF [auth B], DB [auth A], DC [auth B], DD [auth B], DE [auth B], DF [auth B], EB [auth A], EC [auth B], ED [auth B], EE [auth B], EF [auth B], FB [auth A], FC [auth B], FD [auth B], FE [auth B], FF [auth B], GB [auth A], GC [auth B], GD [auth B], GE [auth B], GF [auth B], HB [auth A], HC [auth B], HD [auth B], HE [auth B], HF [auth B], IB [auth A], IC [auth B], ID [auth B], IE [auth B], IF [auth B], JB [auth A], JC [auth B], JD [auth B], JE [auth B], JF [auth B], KB [auth A], KC [auth B], KD [auth B], KE [auth B], KF [auth B], LB [auth A], LC [auth B], LD [auth B], LE [auth B], LF [auth B], MB [auth A], MC [auth B], MD [auth B], ME [auth B], MF [auth B], NB [auth A], NC [auth B], ND [auth B], NE [auth B], NF [auth B], OB [auth A], OC [auth B], OD [auth B], OE [auth B], OF [auth B], PB [auth A], PC [auth B], PD [auth B], PE [auth B], PF [auth B], QB [auth A], QC [auth B], QD [auth B], QE [auth B], QF [auth B], RB [auth A], RC [auth B], RD [auth B], RE [auth B], RF [auth B], SB [auth A], SC [auth B], SD [auth B], SE [auth B], SF [auth B], TB [auth A], TC [auth B], TD [auth B], TE [auth B], TF [auth B], UB [auth A], UC [auth B], UD [auth B], UE [auth B], UF [auth B], VB [auth A], VC [auth B], VD [auth B], VE [auth B], VF [auth B], WB [auth A], WC [auth B], WD [auth B], WE [auth B], WF [auth B], XB [auth A], XC [auth B], XD [auth B], XE [auth B], XF [auth B], YB [auth A], YC [auth B], YD [auth B], YE [auth B], YF [auth C], ZB [auth A], ZC [auth B], ZD [auth B], ZE [auth B], ZF [auth C]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Health and Medical Research Council (NHMRC, Australia)Australia1092262
    European Research Council (ERC)European Union322581 (NOVRIB)

    Revision History  (Full details and data files)

    • Version 1.0: 2017-05-24
      Type: Initial release
    • Version 1.1: 2017-09-20
      Changes: Author supporting evidence, Data collection
    • Version 1.2: 2019-12-18
      Changes: Advisory, Author supporting evidence, Derived calculations, Other