1LU3 | pdb_00001lu3

Separate Fitting of the Anticodon Loop Region of tRNA (nucleotide 26-42) in the Low Resolution Cryo-EM Map of an EF-Tu Ternary Complex (GDP and Kirromycin) Bound to E. coli 70S Ribosome

• PDB DOI: https://doi.org/10.2210/pdb1LU3/pdb
• EM Map EMD-1045: EMDB EMDataResource
• NAKB: 1LU3

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


• Deposited: 2002-05-21 Released: 2002-06-26 
• Deposition Author(s): Valle, M., Sengupta, J., Swami, N.K., Grassucci, R.A., Burkhardt, N., Nierhaus, K.H., Agrawal, R.K., Frank, J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 16.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.

Valle, M., Sengupta, J., Swami, N.K., Grassucci, R.A., Burkhardt, N., Nierhaus, K.H., Agrawal, R.K., Frank, J.

(2002) EMBO J 21: 3557-3567

• PubMed: 12093756 
• DOI: https://doi.org/10.1093/emboj/cdf326


• PubMed Abstract: 
  

  During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.47 kDa 
• Atom Count: 365 
• Modeled Residue Count: 17 
• Deposited Residue Count: 17 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PHENYLALANINE TRANSFER RNA	A	17	Saccharomyces cerevisiae

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 16.8 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-26 
Deposition Author(s): Valle, M., Sengupta, J., Swami, N.K., Grassucci, R.A., Burkhardt, N., Nierhaus, K.H., Agrawal, R.K., Frank, J.

Revision History  

• Version 1.0: 2002-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description