5AN9

Mechanism of eIF6 release from the nascent 60S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1038/nsmb.3112
  • Structures With Same Primary Citation

  • 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

    Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L3A398Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl3DDB_G0291862
Find proteins for P34113 (Dictyostelium discoideum)
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Go to UniProtKB:  P34113
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L9B188Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl9DDB_G0278959
Find proteins for Q54XI5 (Dictyostelium discoideum)
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Go to UniProtKB:  Q54XI5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ACIDIC RIBOSOMAL PROTEIN P0C205Dictyostelium discoideumMutation(s): 0 
Gene Names: rplp0DDB_G0286501
Find proteins for P22685 (Dictyostelium discoideum)
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Go to UniProtKB:  P22685
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L12D166Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl12DDB_G0288295
Find proteins for Q54J50 (Dictyostelium discoideum)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L23E136Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl23DDB_G0290315
Find proteins for Q54G86 (Dictyostelium discoideum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L10F217Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl10rpl10eDDB_G0288273
Find proteins for Q54J69 (Dictyostelium discoideum)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L24G69Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl24DDB_G0280229
Find proteins for Q54VN6 (Dictyostelium discoideum)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-60S RIBOSOMAL PROTEIN L40H52Dictyostelium discoideumMutation(s): 0 
Gene Names: ubqBDDB_G0280755
Find proteins for P14794 (Dictyostelium discoideum)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 6I224Dictyostelium discoideumMutation(s): 0 
Gene Names: eif6DDB_G0276493
Find proteins for Q551M2 (Dictyostelium discoideum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RIBOSOME MATURATION PROTEIN SBDSJ250Homo sapiensMutation(s): 0 
Gene Names: SBDSCGI-97
Find proteins for Q9Y3A5 (Homo sapiens)
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Go to UniProtKB:  Q9Y3A5
NIH Common Fund Data Resources
PHAROS  Q9Y3A5
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  • Reference Sequence

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Entity ID: 11
MoleculeChainsLengthOrganism
26S RIBOSOMAL RNAN3741Dictyostelium discoideum
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2017-04-19
    Changes: Other
  • Version 2.0: 2017-08-02
    Changes: Atomic model, Data collection, Derived calculations