7NWI image
Entry Detail
PDB ID:
7NWI
EMDB ID:
Keywords:
Title:
Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin S
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-03-16
Release Date:
2021-07-07
Method Details:
Experimental Method:
Resolution:
3.13 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Sec61Beta
Chain IDs:ZB (auth: 1)
Chain Length:15
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:P-Site tRNA
Chain IDs:AC (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:28S ribosomal RNA+BlaS
Chain IDs:BC (auth: 5)
Chain Length:3788
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:CC (auth: 7)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:DC (auth: 8)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:18S ribosomal RNA
Chain IDs:EC (auth: 9)
Chain Length:1777
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L8
Chain IDs:A
Chain Length:160
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:SA (auth: AA)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uL3
Chain IDs:B
Chain Length:403
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:TA (auth: BB)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:C
Chain Length:115
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:UA (auth: CC)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:D
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:VA (auth: DD)
Chain Length:53
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:E
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S4
Chain IDs:WA (auth: EE)
Chain Length:262
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uL30
Chain IDs:F
Chain Length:249
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S5
Chain IDs:XA (auth: FF)
Chain Length:205
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:G
Chain Length:241
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:YA (auth: GG)
Chain Length:262
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L9
Chain IDs:H
Chain Length:122
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein eS7
Chain IDs:ZA (auth: HH)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10
Chain IDs:I
Chain Length:117
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:AB (auth: II)
Chain Length:206
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L11
Chain IDs:J
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:BB (auth: JJ)
Chain Length:194
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:FC (auth: K)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S10_plectin domain-containing protein
Chain IDs:CB (auth: KK)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L13
Chain IDs:K (auth: L)
Chain Length:211
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:DB (auth: LL)
Chain Length:158
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L14
Chain IDs:L (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:EB (auth: MM)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L15
Chain IDs:M (auth: N)
Chain Length:23
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein uS15
Chain IDs:FB (auth: NN)
Chain Length:150
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L13a
Chain IDs:N (auth: O)
Chain Length:142
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S14
Chain IDs:GB (auth: OO)
Chain Length:168
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L17
Chain IDs:O (auth: P)
Chain Length:91
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS19
Chain IDs:HB (auth: PP)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal_L18e/L15P domain-containing protein
Chain IDs:P (auth: Q)
Chain Length:188
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Rps16 protein
Chain IDs:IB (auth: QQ)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:Q (auth: R)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S17
Chain IDs:JB (auth: RR)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L18a
Chain IDs:R (auth: S)
Chain Length:318
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein uS13
Chain IDs:KB (auth: SS)
Chain Length:137
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL21
Chain IDs:S (auth: T)
Chain Length:163
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S19
Chain IDs:LB (auth: TT)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22
Chain IDs:T (auth: U)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal_S10 domain-containing protein
Chain IDs:MB (auth: UU)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL14
Chain IDs:U (auth: V)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S21
Chain IDs:NB (auth: VV)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24-like protein
Chain IDs:V (auth: W)
Chain Length:134
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S15a
Chain IDs:OB (auth: WW)
Chain Length:139
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uL23
Chain IDs:W (auth: X)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S23
Chain IDs:PB (auth: XX)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L26
Chain IDs:X (auth: Y)
Chain Length:134
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:QB (auth: YY)
Chain Length:146
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:Y (auth: Z)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:RB (auth: ZZ)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uL15
Chain IDs:Z (auth: a)
Chain Length:160
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:SB (auth: aa)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:AA (auth: b)
Chain Length:403
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:TB (auth: bb)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL30
Chain IDs:BA (auth: c)
Chain Length:115
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:UB (auth: cc)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL31
Chain IDs:CA (auth: d)
Chain Length:107
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein uS14
Chain IDs:VB (auth: dd)
Chain Length:53
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL32
Chain IDs:DA (auth: e)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:WB (auth: ee)
Chain Length:262
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL33
Chain IDs:EA (auth: f)
Chain Length:249
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:S27a
Chain IDs:XB (auth: ff)
Chain Length:205
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:FA (auth: g)
Chain Length:241
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein RACK1
Chain IDs:YB (auth: gg)
Chain Length:262
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uL29
Chain IDs:GA (auth: h)
Chain Length:122
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:HA (auth: i)
Chain Length:117
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L37
Chain IDs:IA (auth: j)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L38
Chain IDs:JA (auth: k)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein eL39
Chain IDs:KA (auth: l)
Chain Length:211
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L40
Chain IDs:LA (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60s ribosomal protein l41
Chain IDs:MA (auth: n)
Chain Length:23
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:LOW QUALITY PROTEIN: 60S ribosomal protein L36a
Chain IDs:NA (auth: o)
Chain Length:142
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:ribosomal protein eL43
Chain IDs:OA (auth: p)
Chain Length:91
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eL28
Chain IDs:PA (auth: r)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S acidic ribosomal protein P0
Chain IDs:QA (auth: s)
Chain Length:318
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:L12
Chain IDs:RA (auth: t)
Chain Length:163
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Primary Citation
Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.
Nucleic Acids Res. 49 7665 7679 (2021)
PMID: 34157102 DOI: 10.1093/nar/gkab532

Abstact

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.

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Primary Citation of related structures