3O1F | pdb_00003o1f

P1 crystal form of E. coli ClpS at 1.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.197 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3O1F

This is version 1.3 of the entry. See complete history

Literature

The ClpS Adaptor Mediates Staged Delivery of N-End Rule Substrates to the AAA+ ClpAP Protease.

Roman-Hernandez, G.Hou, J.Y.Grant, R.A.Sauer, R.T.Baker, T.A.

(2011) Mol Cell 43: 217-228

  • DOI: https://doi.org/10.1016/j.molcel.2011.06.009
  • Primary Citation Related Structures: 
    3O1F, 3O2B, 3O2H, 3O2O

  • PubMed Abstract: 

    The ClpS adaptor delivers N-end rule substrates to ClpAP, an energy-dependent AAA+ protease, for degradation. How ClpS binds specific N-end residues is known in atomic detail and clarified here, but the delivery mechanism is poorly understood. We show that substrate binding is enhanced when ClpS binds hexameric ClpA. Reciprocally, N-end rule substrates increase ClpS affinity for ClpA(6). Enhanced binding requires the N-end residue and a peptide bond of the substrate, as well as multiple aspects of ClpS, including a side chain that contacts the substrate α-amino group and the flexible N-terminal extension (NTE). Finally, enhancement also needs the N domain and AAA+ rings of ClpA, connected by a long linker. The NTE can be engaged by the ClpA translocation pore, but ClpS resists unfolding/degradation. We propose a staged-delivery model that illustrates how intimate contacts between the substrate, adaptor, and protease reprogram specificity and coordinate handoff from the adaptor to the protease.


  • Organizational Affiliation
    • Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Macromolecule Content 

  • Total Structure Weight: 18.6 kDa 
  • Atom Count: 1,716 
  • Modeled Residue Count: 162 
  • Deposited Residue Count: 162 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease adapter protein clpS81Escherichia coliMutation(s): 0 
Gene Names: clpS
UniProt
Find proteins for P0A8Q6 (Escherichia coli (strain K12))
Explore P0A8Q6 
Go to UniProtKB:  P0A8Q6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8Q6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease adapter protein clpS81Escherichia coliMutation(s): 0 
Gene Names: clpS
UniProt
Find proteins for P0A8Q6 (Escherichia coli (strain K12))
Explore P0A8Q6 
Go to UniProtKB:  P0A8Q6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8Q6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SME
Query on SME
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.197 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.025α = 80.5
b = 28.051β = 77.88
c = 51.624γ = 72.3
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2011-08-17
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary