6ZVH

EDF1-ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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: https://doi.org/10.7554/eLife.58828
  • Primary Citation of Related Structures:  
    6ZVH, 6ZVI

  • 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. 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth A]221Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3227Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoform262Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7G [auth H]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth I]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10I [auth K]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11J [auth L]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15K [auth P]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16L [auth Q]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17M [auth R]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18N [auth S]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19O [auth T]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20P [auth U]104Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Q [auth V]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23R [auth X]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26S [auth a]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28T [auth c]64Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29U [auth d]55Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1V [auth g]313Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2W [auth C]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6X [auth G]237Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Y [auth J]185Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12Z [auth M]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13AA [auth N]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14BA [auth O]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aCA [auth W]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24DA [auth Y]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25EA [auth Z]75Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27FA [auth b]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30GA [auth e]42Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aHA [auth f]67Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cell growth-regulating nucleolar proteinJA [auth y]72Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145220 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelial differentiation-related factor 1KA [auth i]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107223 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 2]1,740Homo sapiens
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Entity ID: 35
MoleculeChains LengthOrganismImage
E-site tRNAIA [auth x]75Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NB [auth a],
OB [auth d],
RB [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
BB [auth 2]
CB [auth 2]
DB [auth 2]
EB [auth 2]
AB [auth 2],
BB [auth 2],
CB [auth 2],
DB [auth 2],
EB [auth 2],
FB [auth 2],
GB [auth 2],
HB [auth 2],
IB [auth 2],
JB [auth 2],
KB [auth 2],
LA [auth 2],
LB [auth 2],
MA [auth 2],
MB [auth 2],
NA [auth 2],
OA [auth 2],
PA [auth 2],
PB [auth G],
QA [auth 2],
QB [auth O],
RA [auth 2],
SA [auth 2],
TA [auth 2],
UA [auth 2],
VA [auth 2],
WA [auth 2],
XA [auth 2],
YA [auth 2],
ZA [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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: 2020-08-19
    Type: Initial release