Crystal structure of the periplasmic chaperone Skp

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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Structure of the periplasmic chaperone Skp suggests functional similarity with cytosolic chaperones despite differing architecture.

Korndorfer, I.P.Dommel, M.K.Skerra, A.

(2004) Nat Struct Mol Biol 11: 1015-1020

  • DOI: https://doi.org/10.1038/nsmb828
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 17-kDa protein (Skp) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesized outer-membrane proteins. Here we present its X-ray structure at a resolution of 2.35 A. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerization domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forceps'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin, although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm.

  • Organizational Affiliation

    Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Seventeen Kilodalton Protein
A, B, C
153Escherichia coliMutation(s): 0 
Gene Names: HLPASKPOMPHB0178C0215Z0190ECS0180SF0168S0171
Find proteins for P0AEU7 (Escherichia coli (strain K12))
Explore P0AEU7 
Go to UniProtKB:  P0AEU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEU7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.985α = 90
b = 83.911β = 90
c = 158.378γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references
  • Version 1.4: 2024-05-22
    Changes: Data collection