2DS5

Structure of the ZBD in the orthorhomibic crystal from


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of SspB-tail Recognition by the Zinc Binding Domain of ClpX.

Park, E.Y.Lee, B.G.Hong, S.B.Kim, H.W.Jeon, H.Song, H.K.

(2007) J Mol Biol 367: 514-526

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.003
  • Primary Citation of Related Structures:  
    2DS5, 2DS6, 2DS7, 2DS8

  • PubMed Abstract: 

    The degradation of ssrA(AANDENYALAA)-tagged proteins in the bacterial cytosol is carried out by the ClpXP protease and is markedly stimulated by the SspB adaptor protein. It has previously been reported that the amino-terminal zinc-binding domain of ClpX (ZBD) is involved in complex formation with the SspB-tail (XB: ClpX-binding motif). In an effort to better understand the recognition of SspB by ClpX and the mechanism of delivery of ssrA-tagged substrates to ClpXP, we have determined the structures of ZBD alone at 1.5, 2.0, and 2.5 A resolution in each different crystal form and also in complex with XB peptide at 1.6 A resolution. The XB peptide forms an antiparallel beta-sheet with two beta-strands of ZBD, and the structure shows a 1:1 stoichiometric complex between ZBD and XB, suggesting that there are two independent SspB-tail-binding sites in ZBD. The high-resolution ZBD:XB complex structure, in combination with biochemical analyses, can account for key determinants in the recognition of the SspB-tail by ClpX and sheds light on the mechanism of delivery of target proteins to the prokaryotic degradation machine.


  • Organizational Affiliation

    School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit clpX
A, B
51Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6H1 (Escherichia coli (strain K12))
Explore P0A6H1 
Go to UniProtKB:  P0A6H1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6H1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.523α = 90
b = 43.399β = 90
c = 67.719γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description