5MDV

Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Translational termination without a stop codon.

James, N.R.Brown, A.Gordiyenko, Y.Ramakrishnan, V.

(2016) Science 354: 1437-1440

  • DOI: 10.1126/science.aai9127
  • Primary Citation of Related Structures:  
    5MDV, 5MDW, 5MDY, 5MDZ

  • PubMed Abstract: 
  • Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3 ...

    Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.


    Organizational Affiliation

    Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative ribosome-rescue factor AF [auth 6]61Escherichia coliMutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 2G [auth 7]365Escherichia coliMutation(s): 0 
Gene Names: prfBsupKb2891JW5847
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Entity ID: 8
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50S ribosomal protein L2H [auth B]273Escherichia 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]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6L [auth F]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L24AA [auth U]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BA [auth V]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L28DA [auth X]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29EA [auth Y]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30FA [auth Z]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L31GA [auth a]70Escherichia coliMutation(s): 0 
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50S ribosomal protein L32HA [auth b]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33IA [auth c]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34JA [auth d]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35KA [auth e]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L36LA [auth f]38Escherichia coliMutation(s): 0 
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30S ribosomal protein S2MA [auth g]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3NA [auth h]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4OA [auth i]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5PA [auth j]167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6QA [auth k]135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7RA [auth l]179Escherichia coliMutation(s): 0 
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30S ribosomal protein S10UA [auth o]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11VA [auth p]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12WA [auth q]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13XA [auth r]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14YA [auth s]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15ZA [auth t]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16AB [auth u]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17BB [auth v]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18CB [auth w]75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19DB [auth x]92Escherichia coliMutation(s): 0 
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30S ribosomal protein S20EB [auth y]87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21FB [auth z]71Escherichia coliMutation(s): 0 
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23S ribosomal RNAA [auth 1]2904Escherichia 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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    mRNAD [auth 4]18Escherichia coli
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    fMet-NH-tRNA(fMet)E [auth 5]78Escherichia coli
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    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FME (Subject of Investigation/LOI)
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    AS [auth 5]N-FORMYLMETHIONINE
    C6 H11 N O3 S
    PYUSHNKNPOHWEZ-YFKPBYRVSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    DS [auth a], FS [auth f]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
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    Download Ideal Coordinates CCD File 
    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 5], 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 5], 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], ES [auth b], 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], GS [auth i], 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 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 2], 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 3], 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 3], 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 5], 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 5]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  3 Unique
    IDChainsTypeFormula2D DiagramParent
    FME
    Query on FME
    E [auth 5]L-PEPTIDE LINKINGC6 H11 N O3 SMET
    MEQ
    Query on MEQ
    G [auth 7]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
    0TD
    Query on 0TD
    WA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.97 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


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

    Revision History  (Full details and data files)

    • Version 1.0: 2016-12-14
      Type: Initial release
    • Version 1.1: 2016-12-21
      Changes: Database references
    • Version 1.2: 2016-12-28
      Changes: Database references
    • Version 1.3: 2017-08-30
      Changes: Author supporting evidence, Data collection, Derived calculations
    • Version 2.0: 2018-10-17
      Changes: Data collection, Polymer sequence, Refinement description, Source and taxonomy
    • Version 2.1: 2019-12-11
      Changes: Advisory, Derived calculations, Other