Crystal structure of SspB-ssrA complex

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine

Song, H.K.Eck, M.J.

(2003) Mol Cell 12: 75-86

  • DOI: https://doi.org/10.1016/s1097-2765(03)00271-5
  • Primary Citation of Related Structures:  
    1OX8, 1OX9

  • PubMed Abstract: 

    In prokaryotes, incomplete or misfolded polypeptides emanating from a stalled ribosome are marked for degradation by the addition of an 11 residue peptide (AANDENYALAA) to their C terminus. Substrates containing this conserved degradation signal, the SsrA tag, are targeted to specific proteases including ClpXP and ClpAP. SspB was originally characterized as a stringent starvation protein and has been found to bind specifically to SsrA-tagged proteins and to enhance recognition of these proteins by the ClpXP degradation machine. Here, we report the crystal structures of SspB alone and in complex with an SsrA peptide. Unexpectedly, SspB exhibits a fold found in Sm-family RNA binding proteins. The dimeric SspB structures explain the key determinants for recognition of the SsrA tag and define a hydrophobic channel that may bind unfolded substrates.

  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stringent starvation protein B108Escherichia coli O157:H7Mutation(s): 0 
Gene Names: SSPB OR B3228 OR Z4586 OR ECS4101
Find proteins for P0AFZ3 (Escherichia coli (strain K12))
Explore P0AFZ3 
Go to UniProtKB:  P0AFZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFZ3
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ssrA8N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.513α = 90
b = 81.524β = 92.83
c = 131.773γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    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: 2024-02-14
    Changes: Data collection, Database references