Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.79 kDa 
• Atom Count: 1000 
• Modelled Residue Count: 123 
• Deposited Residue Count: 144 
• Unique protein chains: 1

1J1H

Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus

• PDB DOI: 10.2210/pdb1J1H/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-04 Released: 2003-02-11 
• Deposition Author(s): Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 11 
• Selection Criteria: on the basis of agreement with the experimental data and van der Waals energy 

Literature

Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus

Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G.

(2003) FEBS Lett 535: 94-100

• PubMed: 12560085 
• DOI: 10.1016/s0014-5793(02)03880-2
• Primary Citation of Related Structures:  
  1J1H


• PubMed Abstract: 
  

Small protein B (SmpB) is required for trans-translation, binding specifically to tmRNA. We show here the solution structure of SmpB from an extremely thermophilic bacterium, Thermus thermophilus HB8, determined by heteronuclear nuclear magnetic resonance methods. The core of the protein consists of an antiparallel beta-barrel twisted up from eight beta-strands, each end of which is capped with the second or third helix, and the first helix is located beside the barrel. Its C-terminal sequence (20 residues), which is rich in basic residues, shows a poorly structured form, as often seen in isolated ribosomal proteins. The results are discussed in relation to the oligonucleotide binding fold.

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Organizational Affiliation: 

Department of Industrial Chemistry, Faculty of Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small Protein B	A	144	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q8RR57 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RR57  Go to UniProtKB:  Q8RR57

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 11 
• Selection Criteria: on the basis of agreement with the experimental data and van der Waals energy 
• OLDERADO: 1J1H Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-04 
• Released Date: 2003-02-11 
Deposition Author(s): Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2003-02-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations