2L15

Solution Structure of Cold Shock Protein CspA Using Combined NMR and CS-Rosetta method


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the best score calculted by CS-Rosetta 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.

Tang, Y.Schneider, W.M.Shen, Y.Raman, S.Inouye, M.Baker, D.Roth, M.J.Montelione, G.T.

(2010) J Struct Funct Genomics 11: 223-232

  • DOI: 10.1007/s10969-010-9095-6

  • PubMed Abstract: 
  • Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidecha ...

    Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using <4 days of data collection and fully automated data analysis methods together with CS-Rosetta. The resulting CspA structure is highly converged and in excellent agreement with the published crystal structure, with a backbone RMSD value of 0.5 Å, an all atom RMSD value of 1.2 Å to the crystal structure for well-defined regions, and RMSD value of 1.1 Å to crystal structure for core, non-solvent exposed sidechain atoms. Cross validation of the structure with (15)N- and (13)C-edited NOESY data obtained with a perdeuterated (15)N, (13)C-enriched (13)CH(3) methyl protonated CspA sample confirms that essentially all of these independently-interpreted NOE-based constraints are already satisfied in each of the 10 CS-Rosetta structures. By these criteria, the CS-Rosetta structure generated by fully automated analysis of data for a perdeuterated sample provides an accurate structure of CspA. This represents a general approach for rapid, automated structure determination of small proteins by NMR.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cold shock protein CspA
A
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: cspA (cspS)
Find proteins for P0A9X9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9X9
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the best score calculted by CS-Rosetta 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance