Biological Assembly 1  

 3D View: Structure | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A1B1C1D1E1F1G1H1I1J1 

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

Macromolecule Content

• Total Structure Weight: 1419.24 kDa 
• Atom Count: 39693 
• Modelled Residue Count: 3067 
• Deposited 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
• EMDataResource: EMD-3145

• Classification: TRANSLATION
• Organism(s): Dictyostelium discoideum, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 3.30 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:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L3	A	398	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl3, DDB_G0291862
UniProt
Find proteins for P34113 (Dictyostelium discoideum) Explore P34113  Go to UniProtKB:  P34113

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L9	B	188	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl9, DDB_G0278959
UniProt
Find proteins for Q54XI5 (Dictyostelium discoideum) Explore Q54XI5  Go to UniProtKB:  Q54XI5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ACIDIC RIBOSOMAL PROTEIN P0	C	205	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rplp0, DDB_G0286501
UniProt
Find proteins for P22685 (Dictyostelium discoideum) Explore P22685  Go to UniProtKB:  P22685

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L12	D	166	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl12, DDB_G0288295
UniProt
Find proteins for Q54J50 (Dictyostelium discoideum) Explore Q54J50  Go to UniProtKB:  Q54J50

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L23	E	136	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl23, DDB_G0290315
UniProt
Find proteins for Q54G86 (Dictyostelium discoideum) Explore Q54G86  Go to UniProtKB:  Q54G86

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L10	F	217	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl10, rpl10e, DDB_G0288273
UniProt
Find proteins for Q54J69 (Dictyostelium discoideum) Explore Q54J69  Go to UniProtKB:  Q54J69

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L24	G	69	Dictyostelium discoideum	Mutation(s): 0  Gene Names: rpl24, DDB_G0280229
UniProt
Find proteins for Q54VN6 (Dictyostelium discoideum) Explore Q54VN6  Go to UniProtKB:  Q54VN6

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-60S RIBOSOMAL PROTEIN L40	H	52	Dictyostelium discoideum	Mutation(s): 0  Gene Names: ubqB, DDB_G0280755
UniProt
Find proteins for P14794 (Dictyostelium discoideum) Explore P14794  Go to UniProtKB:  P14794

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
EUKARYOTIC TRANSLATION INITIATION FACTOR 6	I	224	Dictyostelium discoideum	Mutation(s): 0  Gene Names: eif6, DDB_G0276493
UniProt
Find proteins for Q551M2 (Dictyostelium discoideum) Explore Q551M2  Go to UniProtKB:  Q551M2

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOME MATURATION PROTEIN SBDS	J	250	Homo sapiens	Mutation(s): 0  Gene Names: SBDS, CGI-97
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3A5 (Homo sapiens) Explore Q9Y3A5  Go to UniProtKB:  Q9Y3A5
PHAROS:  Q9Y3A5 GTEx:  ENSG00000126524

Entity ID: 11
Molecule	Chains	Length	Organism	Image
26S RIBOSOMAL RNA	K [auth N]	3741	Dictyostelium discoideum

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 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
  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