5M1J

Nonstop ribosomal complex bound with Dom34 and Hbs1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution.

Hilal, T.Yamamoto, H.Loerke, J.Burger, J.Mielke, T.Spahn, C.M.

(2016) Nat Commun 7: 13521-13521

  • DOI: 10.1038/ncomms13521
  • Primary Citation of Related Structures:  
    5M1J

  • PubMed Abstract: 
  • The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling ...

    The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy. The structure shows that Domain N of Dom34 is inserted into the upstream mRNA-binding groove via direct stacking interactions with conserved nucleotides of 18S rRNA. It senses the absence of mRNA at the A-site and part of the mRNA entry channel by direct competition. Thus, our analysis establishes the structural foundation for the recognition of aberrantly stalled 80S ribosomes by the Dom34·Hbs1·GTP complex during Dom34-mediated mRNA surveillance pathways.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein DOM34 A1381Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DOM34YNL001WN2016
EC: 3.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-A A2207Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-B a298Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-A B2214Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-A b281Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2 C2217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-B c263Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3 D2223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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40S ribosomal protein S29-A d253Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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40S ribosomal protein S4-A E2260Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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40S ribosomal protein S30-A e260Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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40S ribosomal protein S5 F2206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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40S ribosomal protein S6-A G2226Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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Guanine nucleotide-binding protein subunit beta-like protein g2318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-A H2184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8-A I2199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-A J2185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10-A K296Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-A L2155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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40S ribosomal protein S12 M2124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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40S ribosomal protein S13 N2150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-A O2127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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40S ribosomal protein S15 P2124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-A Q2141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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40S ribosomal protein S17-B R2125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-A S2145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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40S ribosomal protein S19-A T2143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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40S ribosomal protein S20 U2107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-A V287Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-A W2129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-A X2144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-A Y2134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-A Z270Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31 f271Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28 a5148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-A A5252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29 b558Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L3 B5386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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60S ribosomal protein L30 c597Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
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60S ribosomal protein L4-A C5361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L5 D5296Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L31-A d5109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L32 e5127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-A f5106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
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60S ribosomal protein L7-A F5222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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60S ribosomal protein L34-A g5112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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60S ribosomal protein L8-A G5233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
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60S ribosomal protein L35-A h5119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
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60S ribosomal protein L9-A H5191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L36-A i599Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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60S ribosomal protein L10 I5220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
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60S ribosomal protein L11-A J5169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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60S ribosomal protein L37-A j587Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
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60S ribosomal protein L38 k577Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
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60S ribosomal protein L39 l550Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L13-A L5193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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Ubiquitin-60S ribosomal protein L40 m552Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L14-A M5136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L15-A N5203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-B o5105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L43-B p591Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L17-A P5183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L18-A Q5185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-A S5172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L22-A U5100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L23-A V5136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L27-A Z5135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L16-A K5197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L41-B n525Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L19-A R5188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L25 X5121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L26-A Y5126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L21-A T5159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L6-A E5175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L24-A W598Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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Protein HBS1 A6611Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HBS1YKR084CYKR404
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Entity ID: 34
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18S ribosomal RNA221798Saccharomyces cerevisiae
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Entity ID: 36
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25S ribosomal RNA143396Saccharomyces cerevisiae
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Entity ID: 37
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5S ribosomal RNA34121Saccharomyces cerevisiae
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Entity ID: 38
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5.8S ribosomal RNA44158Saccharomyces cerevisiae
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  • Entity ID: 81
    MoleculeChainsLengthOrganismImage
    nonstop mRNAX720synthetic construct
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    Entity ID: 82
    MoleculeChainsLengthOrganismImage
    yeast Phe-tRNA-PheA376Saccharomyces cerevisiae
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

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    A6
    PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    5CR
    Query on 5CR

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    A3
    N-acetyl-L-phenylalanine
    C11 H13 N O3
    CBQJSKKFNMDLON-JTQLQIEISA-N
     Ligand Interaction
    ZN
    Query on ZN

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    a2, b2, d2, f2, j5, m5, o5, p5
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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