3IZD

Model of the large subunit RNA expansion segment ES27L-out based on a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome. 3IZD is a small part (an expansion segment) which is in an alternative conformation to what is in already 3IZF.

• PDB DOI: https://doi.org/10.2210/pdb3IZD/pdb
• EM Map EMD-1667: EMDB EMDataResource
• NAKB: 3IZD

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2010-10-13 Released: 2010-12-01 
• Deposition Author(s): Armache, J.-P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soeding, J., Westhof, E., Wilson, D.N., Beckmann, R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.

Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soding, J., Westhof, E., Wilson, D.N., Beckmann, R.

(2010) Proc Natl Acad Sci U S A 107: 19748-19753

• PubMed: 20980660 
• DOI: https://doi.org/10.1073/pnas.1009999107
• Primary Citation of Related Structures:  
  3IZD, 4V6I


• PubMed Abstract: 
  

  Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.

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Organizational Affiliation: 

Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.72 kDa 
• Atom Count: 3,044 
• Modelled Residue Count: 151 
• Deposited Residue Count: 151 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
rRNA expansion segment ES27L in an "out" conformation	A	151	Saccharomyces cerevisiae

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Armache, J.-P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soeding, J., Westhof, E., Wilson, D.N., Beckmann, R.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-30
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references