6Q97

Structure of tmRNA SmpB bound in A site of E. coli 70S ribosome

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-12-17 Released: 2019-03-13 
  • Deposition Author(s): Rae, C.D.
  • Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

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 1.0 of the entry. See complete history


Literature

How a circularized tmRNA moves through the ribosome.

Rae, C.D.Gordiyenko, Y.Ramakrishnan, V.

(2019) Science 363: 740-744

  • DOI: 10.1126/science.aav9370
  • Primary Citation of Related Structures:  
    6Q95, 6Q97, 6Q98, 6Q9A

  • PubMed Abstract: 
  • During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3 ...

    During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK. ramak@mrc-lmb.cam.ac.uk.



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Entity ID: 4
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SsrA-binding proteinD [auth 5]145Escherichia coliMutation(s): 0 
Gene Names: smpBsmqBb2620JW2601
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Nascent peptideE [auth 6]28Escherichia coliMutation(s): 0 
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50S ribosomal protein L2H [auth B]270Escherichia coliMutation(s): 0 
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50S ribosomal protein L3I [auth C]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4J [auth D]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5K [auth E]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6L [auth F]175Escherichia coliMutation(s): 0 
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50S ribosomal protein L28DA [auth X]77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29EA [auth Y]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L30FA [auth Z]56Escherichia coliMutation(s): 0 
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50S ribosomal protein L34JA [auth d]46Escherichia coliMutation(s): 0 
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30S ribosomal protein S2MA [auth g]225Escherichia coliMutation(s): 0 
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30S ribosomal protein S6QA [auth k]104Escherichia coliMutation(s): 0 
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30S ribosomal protein S7RA [auth l]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S9TA [auth n]126Escherichia coliMutation(s): 0 
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30S ribosomal protein S10UA [auth o]99Escherichia coliMutation(s): 0 
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30S ribosomal protein S11VA [auth p]117Escherichia coliMutation(s): 0 
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30S ribosomal protein S13XA [auth r]115Escherichia coliMutation(s): 0 
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30S ribosomal protein S14YA [auth s]100Escherichia coliMutation(s): 0 
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23S ribosomal RNAA [auth 1]2903Escherichia coli
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16S ribosomal RNAB [auth 2]1534Escherichia coli
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5S ribosomal RNAC [auth 3]120Escherichia coli
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tRNA-MetF [auth 8]77Escherichia coli
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    transfer-messenger RNA (tmRNA)GB [auth 4]363Escherichia coli
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    ZN
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    BS [auth a], CS [auth f]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
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    MG
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    AC [auth 1] , AD [auth 1] , AE [auth 1] , AF [auth 1] , AG [auth 1] , AH [auth 1] , AI [auth 1] , AJ [auth 1] , 
    AC [auth 1], AD [auth 1], AE [auth 1], AF [auth 1], AG [auth 1], AH [auth 1], AI [auth 1], AJ [auth 1], AK [auth 1], AL [auth 1], AM [auth 1], AN [auth 2], AO [auth 2], AP [auth 2], AQ [auth 2], AR [auth 2], AS [auth X], BC [auth 1], BD [auth 1], BE [auth 1], BF [auth 1], BG [auth 1], BH [auth 1], BI [auth 1], BJ [auth 1], BK [auth 1], BL [auth 1], BM [auth 1], BN [auth 2], BO [auth 2], BP [auth 2], BQ [auth 2], BR [auth 2], CC [auth 1], CD [auth 1], CE [auth 1], CF [auth 1], CG [auth 1], CH [auth 1], CI [auth 1], CJ [auth 1], CK [auth 1], CL [auth 1], CM [auth 1], CN [auth 2], CO [auth 2], CP [auth 2], CQ [auth 2], CR [auth 2], DC [auth 1], DD [auth 1], DE [auth 1], DF [auth 1], DG [auth 1], DH [auth 1], DI [auth 1], DJ [auth 1], DK [auth 1], DL [auth 1], DM [auth 1], DN [auth 2], DO [auth 2], DP [auth 2], DQ [auth 2], DR [auth 2], DS [auth y], EC [auth 1], ED [auth 1], EE [auth 1], EF [auth 1], EG [auth 1], EH [auth 1], EI [auth 1], EJ [auth 1], EK [auth 1], EL [auth 1], EM [auth 1], EN [auth 2], EO [auth 2], EP [auth 2], EQ [auth 2], ER [auth 2], ES [auth 7], FC [auth 1], FD [auth 1], FE [auth 1], FF [auth 1], FG [auth 1], FH [auth 1], FI [auth 1], FJ [auth 1], FK [auth 1], FL [auth 1], FM [auth 1], FN [auth 2], FO [auth 2], FP [auth 2], FQ [auth 2], FR [auth 2], FS [auth 7], GC [auth 1], GD [auth 1], GE [auth 1], GF [auth 1], GG [auth 1], GH [auth 1], GI [auth 1], GJ [auth 1], GK [auth 1], GL [auth 1], GM [auth 1], GN [auth 2], GO [auth 2], GP [auth 2], GQ [auth 2], GR [auth 2], GS [auth 7], HC [auth 1], HD [auth 1], HE [auth 1], HF [auth 1], HG [auth 1], HH [auth 1], HI [auth 1], HJ [auth 1], HK [auth 1], HL [auth 1], HM [auth 1], HN [auth 2], HO [auth 2], HP [auth 2], HQ [auth 2], HR [auth 2], IB [auth 1], IC [auth 1], ID [auth 1], IE [auth 1], IF [auth 1], IG [auth 1], IH [auth 1], II [auth 1], IJ [auth 1], IK [auth 1], IL [auth 1], IM [auth 1], IN [auth 2], IO [auth 2], IP [auth 2], IQ [auth 2], IR [auth 2], JB [auth 1], JC [auth 1], JD [auth 1], JE [auth 1], JF [auth 1], JG [auth 1], JH [auth 1], JI [auth 1], JJ [auth 1], JK [auth 1], JL [auth 1], JM [auth 1], JN [auth 2], JO [auth 2], JP [auth 2], JQ [auth 2], JR [auth 2], KB [auth 1], KC [auth 1], KD [auth 1], KE [auth 1], KF [auth 1], KG [auth 1], KH [auth 1], KI [auth 1], KJ [auth 1], KK [auth 1], KL [auth 1], KM [auth 1], KN [auth 2], KO [auth 2], KP [auth 2], KQ [auth 2], KR [auth 2], LB [auth 1], LC [auth 1], LD [auth 1], LE [auth 1], LF [auth 1], LG [auth 1], LH [auth 1], LI [auth 1], LJ [auth 1], LK [auth 1], LL [auth 1], LM [auth 1], LN [auth 2], LO [auth 2], LP [auth 2], LQ [auth 2], LR [auth 2], MB [auth 1], MC [auth 1], MD [auth 1], ME [auth 1], MF [auth 1], MG [auth 1], MH [auth 1], MI [auth 1], MJ [auth 1], MK [auth 1], ML [auth 1], MM [auth 1], MN [auth 2], MO [auth 2], MP [auth 2], MQ [auth 2], MR [auth 2], NB [auth 1], NC [auth 1], ND [auth 1], NE [auth 1], NF [auth 1], NG [auth 1], NH [auth 1], NI [auth 1], NJ [auth 1], NK [auth 1], NL [auth 1], NM [auth 1], NN [auth 2], NO [auth 2], NP [auth 2], NQ [auth 2], NR [auth 2], OB [auth 1], OC [auth 1], OD [auth 1], OE [auth 1], OF [auth 1], OG [auth 1], OH [auth 1], OI [auth 1], OJ [auth 1], OK [auth 1], OL [auth 1], OM [auth 1], ON [auth 2], OO [auth 2], OP [auth 2], OQ [auth 2], OR [auth 3], PB [auth 1], PC [auth 1], PD [auth 1], PE [auth 1], PF [auth 1], PG [auth 1], PH [auth 1], PI [auth 1], PJ [auth 1], PK [auth 1], PL [auth 1], PM [auth 1], PN [auth 2], PO [auth 2], PP [auth 2], PQ [auth 2], PR [auth 3], QB [auth 1], QC [auth 1], QD [auth 1], QE [auth 1], QF [auth 1], QG [auth 1], QH [auth 1], QI [auth 1], QJ [auth 1], QK [auth 1], QL [auth 1], QM [auth 2], QN [auth 2], QO [auth 2], QP [auth 2], QQ [auth 2], QR [auth 3], RB [auth 1], RC [auth 1], RD [auth 1], RE [auth 1], RF [auth 1], RG [auth 1], RH [auth 1], RI [auth 1], RJ [auth 1], RK [auth 1], RL [auth 1], RM [auth 2], RN [auth 2], RO [auth 2], RP [auth 2], RQ [auth 2], RR [auth 3], SB [auth 1], SC [auth 1], SD [auth 1], SE [auth 1], SF [auth 1], SG [auth 1], SH [auth 1], SI [auth 1], SJ [auth 1], SK [auth 1], SL [auth 1], SM [auth 2], SN [auth 2], SO [auth 2], SP [auth 2], SQ [auth 2], SR [auth 3], TB [auth 1], TC [auth 1], TD [auth 1], TE [auth 1], TF [auth 1], TG [auth 1], TH [auth 1], TI [auth 1], TJ [auth 1], TK [auth 1], TL [auth 1], TM [auth 2], TN [auth 2], TO [auth 2], TP [auth 2], TQ [auth 2], TR [auth 3], UB [auth 1], UC [auth 1], UD [auth 1], UE [auth 1], UF [auth 1], UG [auth 1], UH [auth 1], UI [auth 1], UJ [auth 1], UK [auth 1], UL [auth 1], UM [auth 2], UN [auth 2], UO [auth 2], UP [auth 2], UQ [auth 2], UR [auth 3], VB [auth 1], VC [auth 1], VD [auth 1], VE [auth 1], VF [auth 1], VG [auth 1], VH [auth 1], VI [auth 1], VJ [auth 1], VK [auth 1], VL [auth 1], VM [auth 2], VN [auth 2], VO [auth 2], VP [auth 2], VQ [auth 2], VR [auth 3], WB [auth 1], WC [auth 1], WD [auth 1], WE [auth 1], WF [auth 1], WG [auth 1], WH [auth 1], WI [auth 1], WJ [auth 1], WK [auth 1], WL [auth 1], WM [auth 2], WN [auth 2], WO [auth 2], WP [auth 2], WQ [auth 2], WR [auth 8], XB [auth 1], XC [auth 1], XD [auth 1], XE [auth 1], XF [auth 1], XG [auth 1], XH [auth 1], XI [auth 1], XJ [auth 1], XK [auth 1], XL [auth 1], XM [auth 2], XN [auth 2], XO [auth 2], XP [auth 2], XQ [auth 2], XR [auth 8], YB [auth 1], YC [auth 1], YD [auth 1], YE [auth 1], YF [auth 1], YG [auth 1], YH [auth 1], YI [auth 1], YJ [auth 1], YK [auth 1], YL [auth 1], YM [auth 2], YN [auth 2], YO [auth 2], YP [auth 2], YQ [auth 2], YR [auth M], ZB [auth 1], ZC [auth 1], ZD [auth 1], ZE [auth 1], ZF [auth 1], ZG [auth 1], ZH [auth 1], ZI [auth 1], ZJ [auth 1], ZK [auth 1], ZL [auth 1], ZM [auth 2], ZN [auth 2], ZO [auth 2], ZP [auth 2], ZQ [auth 2], ZR [auth Q]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    0TD
    Query on 0TD
    WA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
    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

    • Deposited Date: 2018-12-17 
    • Released Date: 2019-03-13 
    • Deposition Author(s): Rae, C.D.

    Funding OrganizationLocationGrant Number
    Medical Research Council (United Kingdom)United KingdomMC_U105184332
    Wellcome TrustUnited KingdomWT096570

    Revision History  (Full details and data files)

    • Version 1.0: 2019-03-13
      Type: Initial release