Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - ABCDEFGHIJ 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 1419237.63 
• Atom Count: 39693 
• Residue Count: 5646 
• Unique protein chains: 10
• Unique nucleic acid chains: 1

5AN9

Mechanism of eIF6 release from the nascent 60S ribosomal subunit

• DOI: 10.2210/pdb5AN9/pdb
• EMDataBank: EMD-3145

• Classification: TRANSLATION
• Organism(s): Dictyostelium discoideum, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2015-09-06 Released: 2015-10-21 
• Deposition Author(s): Weis, F., Giudice, E., Churcher, M., Jin, L., Hilcenko, C., Wong, C.C., Traynor, D., Kay, R.R., Warren, A.J.

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Experimental Data Snapshot

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

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

• PubMed: 26479198 
• DOI: 10.1038/nsmb.3112
• Primary Citation of Related Structures:  
  5ANC, 5ANB


• 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.

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Organizational Affiliation: 

Cambridge Institute for Medical Research, Cambridge, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
60S RIBOSOMAL PROTEIN L3	A	398	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl3
Find proteins for P34113 (Dictyostelium discoideum) Go to UniProtKB:  P34113

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
60S RIBOSOMAL PROTEIN L9	B	188	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl9
Find proteins for Q54XI5 (Dictyostelium discoideum) Go to UniProtKB:  Q54XI5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
60S ACIDIC RIBOSOMAL PROTEIN P0	C	205	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rplp0
Find proteins for P22685 (Dictyostelium discoideum) Go to UniProtKB:  P22685

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
60S RIBOSOMAL PROTEIN L12	D	166	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl12
Find proteins for Q54J50 (Dictyostelium discoideum) Go to UniProtKB:  Q54J50

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
60S RIBOSOMAL PROTEIN L23	E	136	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl23
Find proteins for Q54G86 (Dictyostelium discoideum) Go to UniProtKB:  Q54G86

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
60S RIBOSOMAL PROTEIN L10	F	217	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl10 (rpl10e)
Find proteins for Q54J69 (Dictyostelium discoideum) Go to UniProtKB:  Q54J69

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
60S RIBOSOMAL PROTEIN L24	G	69	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl24
Find proteins for Q54VN6 (Dictyostelium discoideum) Go to UniProtKB:  Q54VN6

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN-60S RIBOSOMAL PROTEIN L40	H	52	Dictyostelium discoideum	Mutation(s): 0  Gene Names: ubqB
Find proteins for P14794 (Dictyostelium discoideum) Go to UniProtKB:  P14794

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
EUKARYOTIC TRANSLATION INITIATION FACTOR 6	I	224	Dictyostelium discoideum	Mutation(s): 0  Gene Names: eif6
Find proteins for Q551M2 (Dictyostelium discoideum) Go to UniProtKB:  Q551M2

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOME MATURATION PROTEIN SBDS	J	250	Homo sapiens	Mutation(s): 0  Gene Names: SBDS
Find proteins for Q9Y3A5 (Homo sapiens) Go to Gene View: SBDS Go to UniProtKB:  Q9Y3A5

Entity ID: 11
Molecule	Chains	Length	Organism
26S RIBOSOMAL RNA	N	3741	Dictyostelium discoideum

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-06 
• Released Date: 2015-10-21 
• Deposition Author(s): Weis, F., Giudice, E., Churcher, M., Jin, L., Hilcenko, C., Wong, C.C., Traynor, D., Kay, R.R., Warren, A.J.

Revision History 

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