6QKL image
Deposition Date 2019-01-29
Release Date 2019-03-20
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6QKL
Keywords:
RIBOSOME
Title:
Mechanism of eIF6 release from the nascent 60S ribosomal subunit
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Dictyostelium discoideum (Taxon ID: 44689)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6QKL validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):rpl3
Chain IDs:B (auth: A)
Chain Length:398
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:P34113 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):rpl9
Chain IDs:C (auth: B)
Chain Length:188
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:Q54XI5 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):rplp0
Chain IDs:J (auth: C)
Chain Length:205
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:P22685 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Gene (Uniprot):rpl12
Chain IDs:K (auth: D)
Chain Length:166
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:Q54J50 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):rpl23
Chain IDs:D (auth: E)
Chain Length:136
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:Q54G86 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):rpl10
Chain IDs:E (auth: F)
Chain Length:217
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:Q54J69 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Gene (Uniprot):rpl24
Chain IDs:F (auth: G)
Chain Length:69
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:Q54VN6 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):ubqB
Chain IDs:G (auth: H)
Chain Length:52
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:P14794 Pfam ID:PF01020
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):eif6
Chain IDs:H (auth: I)
Chain Length:224
Number of Molecules:1
Biological Source:Dictyostelium discoideum
UniProt ID:Q551M2 Pfam ID:PF01912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome maturation protein SBDS
Gene (Uniprot):SBDS
Chain IDs:I (auth: J)
Chain Length:250
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3A5 Pfam ID:PF01172, PF09377, PF20268
Polymer Type:polyribonucleotide
Molecule:26S RIBOSOMAL RNA
Chain IDs:A (auth: N)
Chain Length:3741
Number of Molecules:1
Biological Source:Dictyostelium discoideum
Ligand Molecules
NA
Primary Citation
Mechanism of eIF6 release from the nascent 60S ribosomal subunit.
Nat.Struct.Mol.Biol. 22 914 919 (2015)
PMID: 26479198 DOI: 10.1038/nsmb.3112

Abstact

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.

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Primary Citation of related structures
6QKL