1U2M | pdb_00001u2m

Crystal Structure of Skp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.259 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of Skp, a Prefoldin-like Chaperone that Protects Soluble and Membrane Proteins from Aggregation

Walton, T.A.Sousa, M.C.

(2004) Mol Cell 15: 367-374

  • DOI: https://doi.org/10.1016/j.molcel.2004.07.023
  • Primary Citation Related Structures: 
    1U2M

  • PubMed Abstract: 

    The Seventeen Kilodalton Protein (Skp) is a trimeric periplasmic chaperone that assists outer membrane proteins in their folding and insertion into membranes. Here we report the crystal structure of Skp from E. coli. The structure of the Skp trimer resembles a jellyfish with alpha-helical tentacles protruding from a beta barrel body defining a central cavity. The architecture of Skp is unexpectedly similar to that of Prefoldin/GimC, a cytosolic chaperone present in eukaria and archea, that binds unfolded substrates in its central cavity. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide (LPS). These interactions are needed for efficient Skp-assisted folding of membrane proteins. We have identified a putative LPS binding site on the outer surface of Skp and propose a model for unfolded substrate binding.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA.

Macromolecule Content 

  • Total Structure Weight: 48.56 kDa 
  • Atom Count: 2,662 
  • Modeled Residue Count: 345 
  • Deposited Residue Count: 429 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-like protein HLP-1
A, B, C
143Escherichia coliMutation(s): 5 
Gene Names: HLPA
UniProt
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
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.259 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.828α = 90
b = 84.19β = 90
c = 160.181γ = 90
Software Package:
Software NamePurpose
CNSrefinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary