7NWG

Mammalian pre-termination 80S ribosome with Hybrid P/E- and A/P-site tRNA's bound by Blasticidin S.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.

Powers, K.T.Stevenson-Jones, F.Yadav, S.K.N.Amthor, B.Bufton, J.C.Borucu, U.Shen, D.Becker, J.P.Lavysh, D.Hentze, M.W.Kulozik, A.E.Neu-Yilik, G.Schaffitzel, C.

(2021) Nucleic Acids Res 49: 7665-7679

  • DOI: 10.1093/nar/gkab532
  • Primary Citation of Related Structures:  
    7NWG, 7NWH, 7NWI

  • PubMed Abstract: 
  • Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit ...

    Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3'CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1's accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.


    Organizational Affiliation

    University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAE [auth B2]295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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Entity ID: 6
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40S ribosomal protein S3aF [auth C2]264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 7
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40S ribosomal protein S2G [auth D2]259Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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40S ribosomal protein S3H [auth E2]281Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
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Entity ID: 9
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S4I [auth F2]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
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Ribosomal protein S5J [auth G2]205Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 11
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40S ribosomal protein S6K [auth H2]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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ribosomal protein eS7L [auth I2]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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40S ribosomal protein S8M [auth J2]206Oryctolagus cuniculusMutation(s): 1 
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40S ribosomal protein S9N [auth K2]194Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S10O [auth L2]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
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40S ribosomal protein S11P [auth M2]158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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40S ribosomal protein S12Q [auth N2]123Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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ribosomal protein uS15R [auth O2]149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
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uS11S [auth P2]168Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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40S ribosomal protein uS19T [auth Q2]145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Ribosomal protein S16U [auth R2]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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40S ribosomal protein S17V [auth S2]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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40S ribosomal protein uS13W [auth T2]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
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S19X [auth U2]145Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S20Y [auth V2]130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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40S ribosomal protein S21Z [auth W2]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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Ribosomal protein S15aAA [auth X2]139Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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Ribosomal protein S23BA [auth Y2]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
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40S ribosomal protein S24CA [auth Z2]146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
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ribosomal protein eS25DA [auth a2]198Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S26EA [auth b2]117Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27FA [auth c2]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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40S ribosomal protein S28GA [auth d2]69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 34
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uS14HA [auth e2]55Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S30IA [auth f2]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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eS31JA [auth g2]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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ribosomal protein RACK1KA [auth h2]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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L8LA [auth A3]246Oryctolagus cuniculusMutation(s): 0 
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uL3MA [auth B3]403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
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uL4NA [auth C3]425Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L5OA [auth D3]297Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6PA [auth E3]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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uL30QA [auth F3]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
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L7aRA [auth G3]241Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1STW0 (Oryctolagus cuniculus)
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L9SA [auth H3]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L10TA [auth I3]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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60S ribosomal protein L11UA [auth J3]181Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 48
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L13VA [auth L3]211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
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Ribosomal protein L14WA [auth M3]218Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Ribosomal protein L15XA [auth N3]203Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL13YA [auth O3]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
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uL22ZA [auth P3]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
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L18AB [auth Q3]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L19BB [auth R3]196Oryctolagus cuniculusMutation(s): 0 
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Find proteins for Q3T0W9 (Bos taurus)
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Entity ID: 55
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60S ribosomal protein L18aCB [auth S3]176Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A287APR1 (Sus scrofa)
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Entity ID: 56
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eL21DB [auth T3]159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 57
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L22EB [auth U3]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
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eL14FB [auth V3]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 59
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uL23GB [auth X3]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 60
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Ribosomal protein L26HB [auth Y3]132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 61
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60S ribosomal protein L27IB [auth Z3]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 62
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uL15JB [auth a3]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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eL29KB [auth b3]245Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 64
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eL30LB [auth c3]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 65
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eL31MB [auth d3]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
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eL32NB [auth e3]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 67
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eL33OB [auth f3]109Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 68
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60S ribosomal protein L34PB [auth g3]126Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 69
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uL29QB [auth h3]122Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 70
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60S ribosomal protein L36RB [auth i3]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
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Ribosomal protein L37SB [auth j3]97Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 72
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L38TB [auth k3]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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eL39UB [auth l3]50Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 74
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60S RIBOSOMAL PROTEIN EL40VB [auth m3]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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60s ribosomal protein l41WB [auth n3]25Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 76
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eL42XB [auth o3]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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ribosomal protein eL43YB [auth p3]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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eL28ZB [auth r3]137Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 80
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60S acidic ribosomal protein P0BC [auth t3]318Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPLP0
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Find proteins for G1SPK4 (Oryctolagus cuniculus)
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Entity ID: 81
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uL12CC [auth u3]195Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
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Ribosomal proteinFC [auth w3]217Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 85
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Sec61BetaGC [auth 1]15Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
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60S ribosomal protein L24-like proteinHC [auth W]134Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A061I3X8 (Cricetulus griseus)
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Entity ID: 1
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28S Ribosomal RNAA [auth 51]3788Oryctolagus cuniculus
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Entity ID: 2
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5S Ribosomal RNAB [auth 71]120Oryctolagus cuniculus
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Entity ID: 3
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5.8S Ribosomal RNAC [auth 81]151Oryctolagus cuniculus
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Entity ID: 4
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18S Ribosomal RNAD [auth A2]1818Oryctolagus cuniculus
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Entity ID: 79
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A/P-Site tRNAAC [auth q3]74Oryctolagus cuniculus
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Entity ID: 82
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mRNADC [auth v3]18Oryctolagus cuniculus
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Entity ID: 83
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P/E-Site tRNAEC [auth 33]75Oryctolagus cuniculus
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLS (Subject of Investigation/LOI)
Query on BLS

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TJ [auth 51]BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
 Ligand Interaction
ZN
Query on ZN

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AO [auth m3],
BO [auth o3],
CN [auth A2],
CO [auth p3],
DN [auth A2],
AO [auth m3],
BO [auth o3],
CN [auth A2],
CO [auth p3],
DN [auth A2],
JN [auth b2],
YN [auth g3],
ZN [auth j3]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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