6QKL

Mechanism of eIF6 release from the nascent 60S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 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

Mechanism of eIF6 release from the nascent 60S ribosomal subunit.

Weis, F.Giudice, E.Churcher, M.Jin, L.Hilcenko, C.Wong, C.C.Traynor, D.Kay, R.R.Warren, A.J.

(2015) Nat.Struct.Mol.Biol. 22: 914-919

  • DOI: 10.1038/nsmb.3112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor e ...

    SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.


    Organizational Affiliation

    Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.,Cambridge Institute for Medical Research, Cambridge, UK.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.,Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK.,Université de Rennes 1, Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 6290, Institut de Génétique et Développement de Rennes, Rennes, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
A
398Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl3
Find proteins for P34113 (Dictyostelium discoideum)
Go to UniProtKB:  P34113
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9
B
188Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl9
Find proteins for Q54XI5 (Dictyostelium discoideum)
Go to UniProtKB:  Q54XI5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
E
136Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl23
Find proteins for Q54G86 (Dictyostelium discoideum)
Go to UniProtKB:  Q54G86
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
F
217Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl10 (rpl10e)
Find proteins for Q54J69 (Dictyostelium discoideum)
Go to UniProtKB:  Q54J69
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24
G
69Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl24
Find proteins for Q54VN6 (Dictyostelium discoideum)
Go to UniProtKB:  Q54VN6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
H
52Dictyostelium discoideumMutation(s): 0 
Gene Names: ubqB
Find proteins for P14794 (Dictyostelium discoideum)
Go to UniProtKB:  P14794
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
I
224Dictyostelium discoideumMutation(s): 0 
Gene Names: eif6
Find proteins for Q551M2 (Dictyostelium discoideum)
Go to UniProtKB:  Q551M2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosome maturation protein SBDS
J
250Homo sapiensMutation(s): 0 
Gene Names: SBDS
Find proteins for Q9Y3A5 (Homo sapiens)
Go to Gene View: SBDS
Go to UniProtKB:  Q9Y3A5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
C
205Dictyostelium discoideumMutation(s): 0 
Gene Names: rplp0
Find proteins for P22685 (Dictyostelium discoideum)
Go to UniProtKB:  P22685
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12
D
166Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl12
Find proteins for Q54J50 (Dictyostelium discoideum)
Go to UniProtKB:  Q54J50
Entity ID: 1
MoleculeChainsLengthOrganism
26S RIBOSOMAL RNAN3741Dictyostelium discoideum
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BloodwiseUnited Kingdom12048
Medical Research Council (United Kingdom)United KingdomMC_U105161083
Wellcome TrustUnited Kingdom100140

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release