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 

wwPDB Validation   3D Report Full Report


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. 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

    Cambridge Institute for Medical Research, Cambridge, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L3398Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for P34113 (Dictyostelium discoideum)
Explore P34113 
Go to UniProtKB:  P34113
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34113
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9188Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54XI5 (Dictyostelium discoideum)
Explore Q54XI5 
Go to UniProtKB:  Q54XI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54XI5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P0205Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for P22685 (Dictyostelium discoideum)
Explore P22685 
Go to UniProtKB:  P22685
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22685
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L12166Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54J50 (Dictyostelium discoideum)
Explore Q54J50 
Go to UniProtKB:  Q54J50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54J50
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23136Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54G86 (Dictyostelium discoideum)
Explore Q54G86 
Go to UniProtKB:  Q54G86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54G86
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10217Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54J69 (Dictyostelium discoideum)
Explore Q54J69 
Go to UniProtKB:  Q54J69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54J69
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L2469Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54VN6 (Dictyostelium discoideum)
Explore Q54VN6 
Go to UniProtKB:  Q54VN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54VN6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L4052Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for P14794 (Dictyostelium discoideum)
Explore P14794 
Go to UniProtKB:  P14794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14794
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 6224Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q551M2 (Dictyostelium discoideum)
Explore Q551M2 
Go to UniProtKB:  Q551M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ551M2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOME MATURATION PROTEIN SBDS250Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3A5 (Homo sapiens)
Explore Q9Y3A5 
Go to UniProtKB:  Q9Y3A5
PHAROS:  Q9Y3A5
GTEx:  ENSG00000126524 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3A5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR TU GTP-BINDING DOMAIN-CONTAINING PROTEIN 11,120Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2Z2 (Homo sapiens)
Explore Q7Z2Z2 
Go to UniProtKB:  Q7Z2Z2
PHAROS:  Q7Z2Z2
GTEx:  ENSG00000140598 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z2Z2
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains LengthOrganismImage
26S RIBOSOMAL RNAL [auth N]3,741Dictyostelium discoideum
Sequence Annotations
Expand
  • Reference Sequence
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

View Full Validation Report



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