5MDY

Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 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:  
    5MDW, 5MDV, 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 coli K-12Mutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 2G [auth 7]378Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0142prfB
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2H [auth B]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3I [auth C]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4J [auth D]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 11
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50S ribosomal protein L5K [auth E]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 12
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50S ribosomal protein L6L [auth F]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 13
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50S ribosomal protein L9M [auth G]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 14
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50S ribosomal protein L10N [auth H]165Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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Entity ID: 15
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50S ribosomal protein L11O [auth I]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 16
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50S ribosomal protein L13P [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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50S ribosomal protein L14Q [auth K]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 18
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50S ribosomal protein L15R [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 19
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50S ribosomal protein L16S [auth M]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 20
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50S ribosomal protein L17T [auth N]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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50S ribosomal protein L18U [auth O]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 22
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50S ribosomal protein L19V [auth P]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 23
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50S ribosomal protein L20W [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 24
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50S ribosomal protein L21X [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 25
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50S ribosomal protein L22Y [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 26
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50S ribosomal protein L23Z [auth T]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 27
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50S ribosomal protein L24AA [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 28
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50S ribosomal protein L25BA [auth V]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 29
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50S ribosomal protein L27CA [auth W]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 30
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50S ribosomal protein L28DA [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 31
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50S ribosomal protein L29EA [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 32
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50S ribosomal protein L30FA [auth Z]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 33
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50S ribosomal protein L31GA [auth a]70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 34
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50S ribosomal protein L32HA [auth b]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 35
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50S ribosomal protein L33IA [auth c]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 36
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50S ribosomal protein L34JA [auth d]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 37
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50S ribosomal protein L35KA [auth e]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36LA [auth f]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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30S ribosomal protein S2MA [auth g]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 40
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30S ribosomal protein S3NA [auth h]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4OA [auth i]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 42
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30S ribosomal protein S5PA [auth j]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 43
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30S ribosomal protein S6QA [auth k]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 44
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30S ribosomal protein S7RA [auth l]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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30S ribosomal protein S8SA [auth m]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9TA [auth n]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10UA [auth o]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11VA [auth p]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12WA [auth q]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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30S ribosomal protein S13XA [auth r]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 51
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30S ribosomal protein S14YA [auth s]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S15ZA [auth t]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 53
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30S ribosomal protein S16AB [auth u]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S17BB [auth v]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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30S ribosomal protein S18CB [auth w]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 56
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30S ribosomal protein S19DB [auth x]92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 57
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30S ribosomal protein S20EB [auth y]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 58
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30S ribosomal protein S21FB [auth z]71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 1]2904Escherichia coli K-12
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Entity ID: 2
MoleculeChainsLengthOrganismImage
16S ribosomal RNAB [auth 2]1534Escherichia coli K-12
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli K-12
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    mRNAD [auth 4]18Escherichia coli
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    fMet-NH-tRNA(fMet)E [auth 5]78Escherichia coli
    Protein Feature View
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    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FME (Subject of Investigation/LOI)
    Query on FME

    Download Ideal Coordinates CCD File 
    JS [auth 5]N-FORMYLMETHIONINE
    C6 H11 N O3 S
    PYUSHNKNPOHWEZ-YFKPBYRVSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    MS [auth a], PS [auth f]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    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],  AS [auth 3],  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 3],  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 3],  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 3],  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 3],  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 3],  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 3],  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],  HS [auth 5],  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],  IS [auth 5],  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],  KS [auth 5],  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],  LS [auth 5],  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 2],  NN [auth 2],  NO [auth 2],  NP [auth 2],  NQ [auth 2],  NR [auth 2],  NS [auth b],  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 2],  OS [auth f],  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 2],  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 2],  QS [auth i],  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 2],  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 2],  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 2],  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 2],  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 2],  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 2],  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 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 2],  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 2]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  2 Unique
    IDChainsTypeFormula2D DiagramParent
    FME
    Query on FME
    E [auth 5]L-PEPTIDE LINKINGC6 H11 N O3 SMET
    0TD
    Query on 0TD
    WA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.35 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: 2016-12-21
      Type: Initial release
    • Version 1.1: 2016-12-28
      Changes: Database references
    • Version 1.2: 2017-08-30
      Changes: Author supporting evidence, Data collection, Derived calculations, Experimental preparation
    • Version 2.0: 2018-10-17
      Changes: Data collection, Polymer sequence, Refinement description
    • Version 2.1: 2019-12-11
      Changes: Advisory, Derived calculations, Other