3J16

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 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

  • 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 recyc ...

    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-Stra├če 25, 81377 Munich, Germany. becker@lmb.uni-muenchen.de




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dom34p
A
386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: DOM34
EC: 3.1.-.-
Find proteins for P33309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33309
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rli1p
B
608Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RLI1
Find proteins for Q03195 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03195
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
F
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30E
E
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
G
312Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPP0 (L10E, RPA0, RPL10E, RPLA0)
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05317
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6E
C
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
H
165Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL12A (RPL15B)
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX53
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24E
I
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
D
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 3
MoleculeChainsLengthOrganism
28S ribosomal RNAJ233Saccharomyces cerevisiae
Entity ID: 4
MoleculeChainsLengthOrganism
18S ribosomal RNAK155Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
P-site tRNAL75Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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