1SG2 | pdb_00001sg2

Crystal structure of the periplasmic chaperone Skp

• PDB DOI: https://doi.org/10.2210/pdb1SG2/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-23 Released: 2004-09-14 
• Deposition Author(s): Korndorfer, I.P., Dommel, M.K., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.279 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.223 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

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

• PubMed: 15361861 
• DOI: https://doi.org/10.1038/nsmb828
• Primary Citation Related Structures: 
  1SG2


• 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.

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Organizational Affiliation: 
• Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 51.13 kDa 
• Atom Count: 3,119 
• Modeled Residue Count: 392 
• Deposited Residue Count: 459 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seventeen Kilodalton Protein	A, B, C	153	Escherichia coli	Mutation(s): 0  Gene Names: HLPA, SKP, OMPH, B0178, C0215, Z0190, ECS0180, SF0168, S0171
UniProt
Find proteins for P0AEU7 (Escherichia coli (strain K12)) Explore P0AEU7  Go to UniProtKB:  P0AEU7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.279 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.223 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.985	α = 90
b = 83.911	β = 90
c = 158.378	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-14 
Deposition Author(s): Korndorfer, I.P., Dommel, M.K., Skerra, A.

Revision History  

• 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