5ANB

Mechanism of eIF6 release from the nascent 60S ribosomal subunit

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.0 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

  • DOI: https://doi.org/10.1038/nsmb.3112
  • Primary Citation of Related Structures:  
    5AN9, 5ANB, 5ANC, 6QKL

  • 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 eIF6 from nascent 60S ribosomal subunits ...

    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 LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L3398Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl3, DDB_G0291862
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Find proteins for P34113 (Dictyostelium discoideum)
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UniProt GroupP34113
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9188Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl9, DDB_G0278959
UniProt
Find proteins for Q54XI5 (Dictyostelium discoideum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P0205Dictyostelium discoideumMutation(s): 0 
Gene Names: rplp0, DDB_G0286501
UniProt
Find proteins for P22685 (Dictyostelium discoideum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L12166Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl12, DDB_G0288295
UniProt
Find proteins for Q54J50 (Dictyostelium discoideum)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23136Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl23, DDB_G0290315
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Find proteins for Q54G86 (Dictyostelium discoideum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10217Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl10, rpl10e, DDB_G0288273
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Find proteins for Q54J69 (Dictyostelium discoideum)
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Entity ID: 7
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60S RIBOSOMAL PROTEIN L2469Dictyostelium discoideumMutation(s): 0 
Gene Names: rpl24, DDB_G0280229
UniProt
Find proteins for Q54VN6 (Dictyostelium discoideum)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L4052Dictyostelium discoideumMutation(s): 0 
Gene Names: ubqB, DDB_G0280755
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Find proteins for P14794 (Dictyostelium discoideum)
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Entity ID: 9
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EUKARYOTIC TRANSLATION INITIATION FACTOR 6224Dictyostelium discoideumMutation(s): 0 
Gene Names: eif6, DDB_G0276493
UniProt
Find proteins for Q551M2 (Dictyostelium discoideum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOME MATURATION PROTEIN SBDS250Homo sapiensMutation(s): 0 
Gene Names: SBDS, CGI-97
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3A5 (Homo sapiens)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGATION FACTOR TU GTP-BINDING DOMAIN-CONTAINING PROTEIN 11,120Homo sapiensMutation(s): 0 
Gene Names: EFL1, EFTUD1, FAM42A
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Entity ID: 12
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26S RIBOSOMAL RNAL [auth N]3,741Dictyostelium discoideum
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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