1OX9 | pdb_00001ox9

Crystal structure of SspB-ssrA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.297 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1OX9

This is version 1.3 of the entry. See complete history. 

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 103.08 kDa 
  • Atom Count: 7,280 
  • Modeled Residue Count: 928 
  • Deposited Residue Count: 928 
  • Unique protein chains: 2

Macromolecules

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|  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
UniProt
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
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ssrA8N/AMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.297 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
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
MOLREPphasing
CNSrefinement

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