1OX8

Crystal structure of SspB

• PDB DOI: https://doi.org/10.2210/pdb1OX8/pdb

• Classification: HYDROLASE ACTIVATOR
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-04-01 Released: 2003-08-26 
• Deposition Author(s): Song, H.K., Eck, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.284 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

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

• PubMed: 12887894 
• 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.05 kDa 
• Atom Count: 1,841 
• Modelled Residue Count: 214 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stringent starvation protein B	A, B	107	Escherichia coli O157:H7	Mutation(s): 2  Gene Names: SSPB OR B3228 OR Z4586 OR ECS4101
UniProt
Find proteins for P0AFZ3 (Escherichia coli (strain K12)) Explore P0AFZ3  Go to UniProtKB:  P0AFZ3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.284 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.116	α = 90
b = 60.116	β = 90
c = 187.984	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
DM	model building
CNS	refinement
HKL-2000	data reduction
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-26 
Deposition Author(s): Song, H.K., Eck, M.J.

Revision History  

• 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: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary