1P9K

THE SOLUTION STRUCTURE OF YBCJ FROM E. COLI REVEALS A RECENTLY DISCOVERED ALFAL MOTIF INVOLVED IN RNA-BINDING

• PDB DOI: https://doi.org/10.2210/pdb1P9K/pdb
• Entry: 1P9K supersedes: 1O09
• BMRB: 5818

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-05-12 Released: 2003-11-25 
• Deposition Author(s): Volpon, L., Lievre, C., Osborne, M.J., Gandhi, S., Iannuzzi, P., Larocque, R., Matte, A., Cygler, M., Gehring, K., Ekiel, I., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Literature

The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding.

Volpon, L., Lievre, C., Osborne, M.J., Gandhi, S., Iannuzzi, P., Larocque, R., Cygler, M., Gehring, K., Ekiel, I.

(2003) J Bacteriol 185: 4204-4210

• PubMed: 12837795 
• DOI: https://doi.org/10.1128/JB.185.14.4204-4210.2003
• Primary Citation of Related Structures:  
  1P9K


• PubMed Abstract: 
  

  The structure of the recombinant Escherichia coli protein YbcJ, a representative of a conserved family of bacterial proteins (COG2501), was determined by nuclear magnetic resonance. The fold of YbcJ identified it as a member of the larger family of S4-like RNA binding domains. These domains bind to structured RNA, such as that found in tRNA, rRNA, and a pseudoknot of mRNA. The structure of YbcJ revealed a highly conserved patch of basic residues, comprising amino acids K26, K38, R55, K56, and K59, which likely participate in RNA binding.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.42 kDa 
• Atom Count: 587 
• Modelled Residue Count: 79 
• Deposited Residue Count: 79 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
orf, hypothetical protein	A	79	Escherichia coli K-12	Mutation(s): 0  Gene Names: ybcJ
UniProt
Find proteins for P0AAS7 (Escherichia coli (strain K12)) Explore P0AAS7  Go to UniProtKB:  P0AAS7

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-25 
Deposition Author(s): Volpon, L., Lievre, C., Osborne, M.J., Gandhi, S., Iannuzzi, P., Larocque, R., Matte, A., Cygler, M., Gehring, K., Ekiel, I., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
• This entry supersedes: 1O09

Revision History  

• Version 1.0: 2003-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references