5H5U

Mechanistic insights into the alternative translation termination by ArfA and RF2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 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

Mechanistic insights into the alternative translation termination by ArfA and RF2

Ma, C.Kurita, D.Li, N.Chen, Y.Himeno, H.Gao, N.

(2017) Nature 541: 550-553

  • DOI: 10.1038/nature20822
  • Primary Citation of Related Structures:  
    5H5U

  • PubMed Abstract: 
  • During cellular translation of messenger RNAs by ribosomes, the translation apparatus sometimes pauses or stalls at the elongation and termination steps. With the exception of programmed stalling, which is usually used by cells for regulatory purpose ...

    During cellular translation of messenger RNAs by ribosomes, the translation apparatus sometimes pauses or stalls at the elongation and termination steps. With the exception of programmed stalling, which is usually used by cells for regulatory purposes, ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate translation capacity. Much ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors, misprocessing of primary transcripts, and undesired mRNA cleavage all contribute to the formation of non-stop mRNAs. Ribosomes stalled at the 3' end of non-stop mRNAs do not undergo normal termination owing to the lack of specific stop-codon recognition by canonical peptide release factors at the A-site decoding centre. In bacteria, the transfer-messenger RNA (tmRNA)-SmpB-mediated trans-translation rescue system reroutes stalled ribosomes to the normal elongation cycle and translation termination. Two additional rescue systems, ArfA-RF2 (refs 13, 14, 15, 16) and ArfB (formerly known as YaeJ), are also present in many bacterial species, but their mechanisms are not fully understood. Here, using cryo-electron microscopy, we characterize the structure of the Escherichia coli 70S ribosome bound with ArfA, the release factor RF2, a short non-stop mRNA and a cognate P-site tRNA. The C-terminal loop of ArfA occupies the mRNA entry channel on the 30S subunit, whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2. Despite the distinct conformation of RF2, its conserved catalytic GGQ motif is precisely positioned next to the CCA-end of the P-site tRNA. These data illustrate a stop-codon surrogate mechanism for ArfA in facilitating the termination of non-stop ribosomal complexes by RF2.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20186Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21270Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative ribosome-rescue factor A372Escherichia coli K-12Mutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
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Entity ID: 4
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Peptide chain release factor 24365Escherichia coli K-12Mutation(s): 0 
Gene Names: prfBsupKb2891JW5847
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C272Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 10
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50S ribosomal protein L3D209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 11
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50S ribosomal protein L4E201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 12
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50S ribosomal protein L5F178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 13
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50S ribosomal protein L6G176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 14
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50S ribosomal protein L9H149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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50S ribosomal protein L10I164Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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50S ribosomal protein L11J141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13K142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 18
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50S ribosomal protein L14L123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15M144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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50S ribosomal protein L16N136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17O127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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50S ribosomal protein L18P117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19Q114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20R117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21S103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22T110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23U100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24V103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25W94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 30
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50S ribosomal protein L27X84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28Y77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 32
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50S ribosomal protein L29Z63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 33
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50S ribosomal protein L30a58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32b56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 35
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50S ribosomal protein L33c54Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34d46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35e64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36f38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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30S ribosomal protein S2i240Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 41
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30S ribosomal protein S3j232Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 42
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30S ribosomal protein S4k205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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30S ribosomal protein S5l166Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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30S ribosomal protein S6m135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7n178Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 46
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30S ribosomal protein S8o129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9p129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 48
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30S ribosomal protein S10q103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11r128Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12s123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 51
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30S ribosomal protein S13t117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 52
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30S ribosomal protein S14u100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 53
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30S ribosomal protein S15v88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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30S ribosomal protein S16w82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S17x83Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 56
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30S ribosomal protein S18y74Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7T7
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  • Reference Sequence
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19z91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
Go to UniProtKB:  P0A7U3
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Entity ID: 5
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P-site tRNA576Escherichia coli
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  • Entity ID: 6
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    mRNA76Escherichia coli
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    Entity ID: 7
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    23S rRNAA2903Escherichia coli K-12
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    Entity ID: 8
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    5S Ribosomal RNAB120Escherichia coli K-12
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    Entity ID: 39
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    16S rRNAh1534Escherichia coli K-12
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.01 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2017-01-25
      Type: Initial release
    • Version 1.1: 2017-02-08
      Changes: Database references
    • Version 1.2: 2018-10-24
      Changes: Data collection, Other, Refinement description