3J2I | pdb_00003j2i

Structure of late pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel

• PDB DOI: https://doi.org/10.2210/pdb3J2I/pdb
• EM Map EMD-5513: EMDB EMDataResource

• Classification: RIBOSOMAL PROTEIN, SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
• Mutation(s): No 


• Deposited: 2012-10-04 Released: 2012-11-07 
• Deposition Author(s): Bradatsch, B., Leidig, C., Granneman, S., Gnaedig, M., Tollervey, D., Boettcher, B., Beckmann, R., Hurt, E.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 11.9 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.

Bradatsch, B., Leidig, C., Granneman, S., Gnadig, M., Tollervey, D., Bottcher, B., Beckmann, R., Hurt, E.

(2012) Nat Struct Mol Biol 19: 1234-1241

• PubMed: 23142978 
• DOI: https://doi.org/10.1038/nsmb.2438
• Primary Citation Related Structures: 
  3J2I


• PubMed Abstract: 
  

  Preribosomal particles evolve in the nucleus through transient interaction with biogenesis factors before export to the cytoplasm. Here, we report the architecture of the late pre-60S particle, purified from Saccharomyces cerevisiae, through Arx1, a nuclear export factor with structural homology to methionine aminopeptidases, or its binding partner Alb1. Cryo-EM reconstruction of the Arx1 particle at 11.9-Å resolution reveals regions of extra density on the pre-60S particle attributed to associated biogenesis factors, confirming the immature state of the nascent subunit. One of these densities could be unambiguously assigned to Arx1. Immunoelectron microscopy and UV cross-linking localize Arx1 close to the ribosomal exit tunnel, in direct contact with ES27, a highly dynamic eukaryotic rRNA expansion segment. The binding of Arx1 at the exit tunnel may position this export factor to prevent premature recruitment of ribosome-associated factors active during translation.

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Organizational Affiliation: 
• Biochemistry Center, Universität Heidelberg, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.33 kDa 
• Atom Count: 4,529 
• Modeled Residue Count: 578 
• Deposited Residue Count: 639 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 6	A [auth B]	245	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12522  Go to UniProtKB:  Q12522

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferation-associated protein 2G4	B [auth A]	394	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ80 (Homo sapiens) Explore Q9UQ80  Go to UniProtKB:  Q9UQ80
PHAROS:  Q9UQ80 GTEx:  ENSG00000170515

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 11.9 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Bradatsch, B., Leidig, C., Granneman, S., Gnaedig, M., Tollervey, D., Boettcher, B., Beckmann, R., Hurt, E.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2012-12-19
  Changes: Database references
• Version 1.3: 2018-07-18
  Changes: Data collection
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references