6Q9A

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

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

  • Deposited: 2018-12-17 Released: 2019-04-17 
  • Deposition Author(s): Rae, C.D.
  • Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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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Nascent peptideD [auth 6]23Escherichia coliMutation(s): 0 
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30S ribosomal protein S7PA [auth l]152Escherichia coliMutation(s): 0 
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30S ribosomal protein S10SA [auth o]99Escherichia coliMutation(s): 0 
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30S ribosomal protein S11TA [auth p]116Escherichia coliMutation(s): 0 
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30S ribosomal protein S12UA [auth q]122Escherichia coliMutation(s): 0 
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30S ribosomal protein S13VA [auth r]116Escherichia coliMutation(s): 0 
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30S ribosomal protein S21DB [auth z]70Escherichia coliMutation(s): 0 
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SsrA-binding proteinEB [auth 5]118Escherichia 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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tmRNAFB [auth 4]363Escherichia coli
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Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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AS [auth f], XR [auth a]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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], 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], BS [auth i], 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], CS [auth s], 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], 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], 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], GB [auth 1], 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], HB [auth 1], 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 3], 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 3], 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 3], 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 2], MN [auth 2], MO [auth 2], MP [auth 2], MQ [auth 2], MR [auth 3], 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 2], NN [auth 2], NO [auth 2], NP [auth 2], NQ [auth 2], NR [auth 3], 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 2], 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 2], 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 7], 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 7], 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 7], 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 7], 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 O], 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 Q], 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], 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 b], 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 f]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
UA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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: 2019-04-17 
  • 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: 2019-04-17
    Type: Initial release