5NP6

70S structure prior to bypassing

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Ribosome rearrangements at the onset of translational bypassing.

Agirrezabala, X., Samatova, E., Klimova, M., Zamora, M., Gil-Carton, D., Rodnina, M.V., Valle, M.

(2017) Sci Adv 3: e1700147-e1700147

  • DOI: https://doi.org/10.1126/sciadv.1700147
  • Primary Citation of Related Structures:  
    5NP6

  • PubMed Abstract: 

    • Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4 ...

    Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNA Gly to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region. Together, PTC conformation and mRNA structure safeguard against premature termination and read-through of the stop codon and reconfigure the ribosome to a state poised for take-off and sliding along the noncoding mRNA gap.

    Organizational Affiliation: 

    Structural Biology Unit, CIC bioGUNE, 48160 Derio, Spain.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase small subunitC46Tequatrovirus T4Mutation(s): 0 
Gene Names: 60
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2E218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsB, b0169, JW0164
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3F206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC, b3314, JW3276
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4G205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5H157Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6I100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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Entity ID: 10
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30S ribosomal protein S7J151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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Entity ID: 11
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30S ribosomal protein S8K129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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Entity ID: 12
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30S ribosomal protein S9L127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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Entity ID: 13
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30S ribosomal protein S10M98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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Entity ID: 14
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30S ribosomal protein S11N116Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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Entity ID: 15
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30S ribosomal protein S12O123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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Entity ID: 16
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30S ribosomal protein S13P114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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Entity ID: 17
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30S ribosomal protein S14Q101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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Entity ID: 18
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30S ribosomal protein S15R88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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Entity ID: 19
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30S ribosomal protein S16S82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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Entity ID: 20
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30S ribosomal protein S17T80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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Entity ID: 21
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30S ribosomal protein S18U65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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30S ribosomal protein S19V79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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Entity ID: 23
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30S ribosomal protein S20W85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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30S ribosomal protein S21X65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsU, b3065, JW3037
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Entity ID: 27
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50S ribosomal protein L2AA [auth a]271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplB, b3317, JW3279
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Entity ID: 28
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50S ribosomal protein L3BA [auth b]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplC, b3320, JW3282
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50S ribosomal protein L4CA [auth c]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplD, eryA, b3319, JW3281
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50S ribosomal protein L5DA [auth d]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplE, b3308, JW3270
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Entity ID: 31
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50S ribosomal protein L6EA [auth e]176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplF, b3305, JW3267
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50S ribosomal protein L9FA [auth f]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplI, b4203, JW4161
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50S ribosomal protein L11GA [auth g]141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplK, relC, b3983, JW3946
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50S ribosomal protein L13HA [auth h]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplM, b3231, JW3200
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50S ribosomal protein L14IA [auth i]122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplN, b3310, JW3272
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50S ribosomal protein L15JA [auth j]143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO, b3301, JW3263
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50S ribosomal protein L16KA [auth k]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplP, b3313, JW3275
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50S ribosomal protein L17LA [auth l]120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQ, b3294, JW3256
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50S ribosomal protein L18MA [auth m]116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplR, b3304, JW3266
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50S ribosomal protein L19NA [auth n]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplS, b2606, JW2587
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50S ribosomal protein L20OA [auth o]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplT, pdzA, b1716, JW1706
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50S ribosomal protein L21PA [auth p]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplU, b3186, JW3153
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50S ribosomal protein L22QA [auth q]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplV, eryB, b3315, JW3277
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50S ribosomal protein L23RA [auth r]93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplW, b3318, JW3280
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50S ribosomal protein L24SA [auth s]102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplX, b3309, JW3271
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50S ribosomal protein L25TA [auth t]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplY, b2185, JW2173
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth u]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmA, b3185, JW3152
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Entity ID: 48
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50S ribosomal protein L28VA [auth v]77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmB, b3637, JW3612
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Entity ID: 49
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50S ribosomal protein L29WA [auth w]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmC, b3312, JW3274
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Entity ID: 50
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50S ribosomal protein L30XA [auth x]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmD, b3302, JW3264
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Entity ID: 51
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50S ribosomal protein L32YA [auth y]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmF, b1089, JW1075
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Entity ID: 52
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50S ribosomal protein L33ZA [auth z]50Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmG, b3636, JW3611
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Entity ID: 53
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50S ribosomal protein L34AB [auth 0]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmH, rimA, ssaF, b3703, JW3680
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Entity ID: 54
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50S ribosomal protein L35BB [auth 1]64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmI, b1717, JW1707
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Entity ID: 55
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50S ribosomal protein L36CB [auth 2]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJ, b3299, JW3261
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Entity ID: 56
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50S ribosomal protein L10DB [auth 3]131Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJ, b3985, JW3948
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Entity ID: 57
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50S ribosomal protein L31EB [auth 4]66Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmE, b3936, JW3907
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Entity ID: 1
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mRNAA29Escherichia coli K-12
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Entity ID: 2
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P-site tRNA-GlyB76Escherichia coli K-12
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Entity ID: 4
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16S ribosomal RNAD1,539Escherichia coli
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Entity ID: 25
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23S ribosomal RNAY2,903Escherichia coli
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Entity ID: 26
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5S ribosomal RNAZ120Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION1.4

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-73560-JIN
Spanish Ministry of Economy and CompetitivenessSpainBFU2015-66326
German Research FoundationGermanySFB860

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references, Structure summary
  • Version 1.2: 2017-08-02
    Changes: Data collection
  • Version 2.0: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations, Polymer sequence