6SGC

Rabbit 80S ribosome stalled on a poly(A) tail


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Mechanism of ribosome stalling during translation of a poly(A) tail.

Chandrasekaran, V.Juszkiewicz, S.Choi, J.Puglisi, J.D.Brown, A.Shao, S.Ramakrishnan, V.Hegde, R.S.

(2019) Nat Struct Mol Biol 26: 1132-1140

  • DOI: 10.1038/s41594-019-0331-x
  • Primary Citation of Related Structures:  
    6SGC

  • PubMed Abstract: 
  • Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably ina ...

    Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome's decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. rhegde@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 2
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uS2 B1295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
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40S ribosomal protein S3a C1264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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uS5 D1293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
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uS5 E1243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 6
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40S ribosomal protein S4 F1263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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Ribosomal protein S5 G1204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 8
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40S ribosomal protein S6 H1249Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7 I1194Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S8 J1208Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted) K1194Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S12 N1132Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_S13_N domain-containing protein O1151Oryctolagus cuniculusMutation(s): 0 
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uS19 Q1145Oryctolagus cuniculusMutation(s): 0 
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eS17 S1135Oryctolagus cuniculusMutation(s): 0 
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eS13 T1152Oryctolagus cuniculusMutation(s): 0 
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eS19 U1145Oryctolagus cuniculusMutation(s): 0 
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eS21 W183Oryctolagus cuniculusMutation(s): 0 
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uS12 Y1143Oryctolagus cuniculusMutation(s): 0 
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eS24 Z1130Oryctolagus cuniculusMutation(s): 0 
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eS25 a1125Oryctolagus cuniculusMutation(s): 0 
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eS26 b1115Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27 c184Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28 d169Oryctolagus cuniculusMutation(s): 0 
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uS14 e156Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S30 f1133Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S27a g1156Oryctolagus cuniculusMutation(s): 0 
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WD_REPEATS_REGION domain-containing protein h1317Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8 A2257Oryctolagus cuniculusMutation(s): 0 
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uL3 B2403Oryctolagus cuniculusMutation(s): 0 
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uL4 C2425Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5 D2297Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6 E2291Oryctolagus cuniculusMutation(s): 0 
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uL30 F2247Oryctolagus cuniculusMutation(s): 0 
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eL8 G2319Oryctolagus cuniculusMutation(s): 0 
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uL6 H2192Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L10 I2214Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11 J2178Oryctolagus cuniculusMutation(s): 0 
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eL13 L2211Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14 M2218Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15 N2204Oryctolagus cuniculusMutation(s): 0 
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uL13 O2203Oryctolagus cuniculusMutation(s): 0 
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uL22 P2184Oryctolagus cuniculusMutation(s): 0 
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eL18 Q2188Oryctolagus cuniculusMutation(s): 0 
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eL19 R2196Oryctolagus cuniculusMutation(s): 0 
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eL20 S2176Oryctolagus cuniculusMutation(s): 0 
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eL21 T2160Oryctolagus cuniculusMutation(s): 0 
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eL22 U2128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
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Ribosomal protein L23 V2140Oryctolagus cuniculusMutation(s): 0 
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TRASH domain-containing protein W2157Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L23eN domain-containing protein X2156Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26 Y2145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L27 Z2136Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L18e/L15P domain-containing protein a2148Oryctolagus cuniculusMutation(s): 0 
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eL29 b2245Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L7Ae domain-containing protein c2115Oryctolagus cuniculusMutation(s): 0 
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eL31 d2125Oryctolagus cuniculusMutation(s): 0 
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eL32 e2135Oryctolagus cuniculusMutation(s): 0 
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eL33 f2110Oryctolagus cuniculusMutation(s): 0 
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eL34 g2116Oryctolagus cuniculusMutation(s): 0 
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uL29 h2123Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36 i2105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37 j297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
eL38 k270Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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eL39 l251Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 73
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eL40 m2102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60s ribosomal protein l41 n225Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
eL42 o2106Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U344 (Oryctolagus cuniculus)
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Entity ID: 76
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eL43 p292Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L28e domain-containing protein r2137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
uL10 s2318Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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Ribosomal protein L12 t2165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
poly-lysine nascent chain XX16Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
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Ribosomal protein B217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
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18S ribosomal RNAA11869Oryctolagus cuniculus
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  • Entity ID: 35
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    polyA mRNAi110Homo sapiens
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    Entity ID: 80
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    28S ribosomal RNA543603Oryctolagus cuniculus
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    Entity ID: 81
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    5S ribosomal RNA74120Oryctolagus cuniculus
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    Entity ID: 82
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    5.8S ribosomal RNA84156Oryctolagus cuniculus
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    Entity ID: 85
    MoleculeChainsLengthOrganismImage
    tRNA (Lys3)23, 3376Oryctolagus cuniculus
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SPD
    Query on SPD

    Download Ideal Coordinates CCD File 
    54
    SPERMIDINE
    C7 H19 N3
    ATHGHQPFGPMSJY-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    b1, e1, g1, g2, j2, m2, o2, p2
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    54, 74, 84, A1, A2, B2, I2, P2, Q2, V2, a2, e2, g2, j2
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.80 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_UP_A022_1007
    Medical Research Council (United Kingdom)United KingdomMC_U105184332
    Wellcome TrustUnited KingdomWT096570
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM51266
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM113078

    Revision History 

    • Version 1.0: 2019-12-04
      Type: Initial release
    • Version 1.1: 2019-12-18
      Changes: Database references