6ZVI

Mbf1-ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

EDF1 coordinates cellular responses to ribosome collisions.

Sinha, N.K.Ordureau, A.Best, K.Saba, J.A.Zinshteyn, B.Sundaramoorthy, E.Fulzele, A.Garshott, D.M.Denk, T.Thoms, M.Paulo, J.A.Harper, W.Bennett, E.J.Beckmann, R.Green, R.

(2020) Elife 9

  • DOI: 10.7554/eLife.58828
  • Primary Citation of Related Structures:  
    6ZVI, 6ZVH

  • PubMed Abstract: 
  • Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes ...

    Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AE [auth i]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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RPS1A isoform 1F [auth j]216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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RPS2 isoform 1G [auth k]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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RPS3 isoform 1H [auth l]223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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40S ribosomal protein S4-AI [auth m]260Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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Rps5pJ [auth n]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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40S ribosomal protein S6-AK [auth o]218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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40S ribosomal protein S7-AL [auth p]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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40S ribosomal protein S8-AM [auth q]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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40S ribosomal protein S9-AN [auth r]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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40S ribosomal protein S10-AO [auth s]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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40S ribosomal protein S11-AP [auth t]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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RPS12 isoform 1Q [auth u]124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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40S ribosomal protein S13R [auth v]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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RPS15 isoform 1S [auth x]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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40S ribosomal protein S16-AT [auth y]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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40S ribosomal protein S17-AU [auth z]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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40S ribosomal protein S18-AV [auth A]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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40S ribosomal protein S19-AW [auth B]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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RPS20 isoform 1X [auth C]101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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40S ribosomal protein S21-AY [auth D]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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RPS22A isoform 1Z [auth E]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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40S ribosomal protein S23-AAA [auth H]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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40S ribosomal protein S24-ABA [auth I]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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RPS25A isoform 1CA [auth J]69Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
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40S ribosomal protein S27-ADA [auth L]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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RPS28A isoform 1EA [auth N]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
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40S ribosomal protein S30-AFA [auth P]46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
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RPS31 isoform 1GA [auth Q]73Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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Guanine nucleotide-binding protein subunit beta-like proteinHA [auth R]313Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
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MBF1 isoform 1IA [auth T]111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
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RPS29A isoform 1JA [auth O]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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40S ribosomal protein S14-BKA [auth w]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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RPS26B isoform 1LA [auth K]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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A/P-site tRNAA [auth d]76Saccharomyces cerevisiae
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Entity ID: 2
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P/E-site tRNAB [auth e]77Saccharomyces cerevisiae
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Entity ID: 3
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mRNAC [auth f]35Saccharomyces cerevisiae
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Entity ID: 4
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18S rRNAD [auth h]1758Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MA [auth L], NA [auth O]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release