3J16

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.

Becker, T.Franckenberg, S.Wickles, S.Shoemaker, C.J.Anger, A.M.Armache, J.-P.Sieber, H.Ungewickell, C.Berninghausen, O.Daberkow, I.Karcher, A.Thomm, M.Hopfner, K.P.Green, R.Beckmann, R.

(2012) Nature 482: 501-506

  • DOI: 10.1038/nature10829
  • Primary Citation of Related Structures:  
    3J15, 3J16

  • PubMed Abstract: 
  • Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined ...

    Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.


    Organizational Affiliation

    Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, University of Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany. becker@lmb.uni-muenchen.de



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dom34pA386Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1
Find proteins for P33309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rli1pB608Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03195 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6F191Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30EG [auth E]63Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10H [auth G]312Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6EI [auth C]236Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11J [auth H]165Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24EK [auth I]137Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-AL [auth D]135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsLengthOrganismImage
28S ribosomal RNAC [auth J]233Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChainsLengthOrganismImage
18S ribosomal RNAD [auth K]155Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChainsLengthOrganismImage
P-site tRNAE [auth L]75Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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N [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
O [auth B], P [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

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M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2012-04-18
    Changes: Database references
  • Version 1.4: 2012-05-30
    Changes: Refinement description, Structure summary