Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.99 kDa 
• Atom Count: 1122 
• Residue Count: 141 
• Unique protein chains: 1

1WKI

solution structure of ribosomal protein L16 from thermus thermophilus HB8

• DOI: 10.2210/pdb1WKI/pdb
• BMRB: 6255

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-05-31 Released: 2004-12-14 
• Deposition Author(s): Nishimura, M., Yoshida, T., Shirouzu, M., Terada, T., Kuramitsu, S., Yokoyama, S., Ohkubo, T., Kobayashi, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 700 
• Conformers Submitted: 30 
• Selection Criteria: target function 

Literature

Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8

Nishimura, M., Yoshida, T., Shirouzu, M., Terada, T., Kuramitsu, S., Yokoyama, S., Ohkubo, T., Kobayashi, Y.

(2004) J Mol Biol 344: 1369-1383

• PubMed: 15561149 
• DOI: 10.1016/j.jmb.2004.10.011
• Primary Citation of Related Structures:  
  1WKI


• PubMed Abstract: 
  

Ribosomal protein L16 is an essential component of the bacterial ribosome. It organizes the architecture of aminoacyl tRNA binding site in the ribosome 50S subunit. The three-dimensional structure of L16 from Thermus thermophilus HB8 was determined by NMR. In solution, L16 forms an alpha+beta sandwich structure combined with two additional beta sheets located at the loop regions connecting the two layers. The terminal regions and a central loop region did not show any specific secondary structure. The structured part of L16 could be superimposed well on the C(alpha) model of L16 determined in the crystal structure of the ribosome 50S subunit. By overlaying the L16 solution structure onto the coordinates of the ribosome crystal structure, we constructed the combined model that represents the ribosome-bound state of L16 in the detailed structure. The model showed that L16 possesses residues in contact with helices 38, 39, 42, 43 and 89 of 23S rRNA and helix 4 of 5S rRNA. This suggests its broad effect on the ribosome architecture. Comparison of L16 with the L10e protein, which is the archaeal counterpart, showed that they share a common fold, but differ in some regions of functional importance, especially in the N-terminal region. All known mutation sites in L16 that confer resistance to avilamycin and evernimicin were positioned so that their side-chains were exposed to solvent in the internal cavity of the ribosome. This suggests the direct participation of L16 as a part of the binding site for antibiotics.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LSU ribosomal protein L16P	A	141	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rplP, TTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore P60489  Go to UniProtKB:  P60489

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 700 
• Conformers Submitted: 30 
• Selection Criteria: target function 
• OLDERADO: 1WKI Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-31 
• Released Date: 2004-12-14 
Deposition Author(s): Nishimura, M., Yoshida, T., Shirouzu, M., Terada, T., Kuramitsu, S., Yokoyama, S., Ohkubo, T., Kobayashi, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance