3O39

Crystal Structure of SPY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.599 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Genetic selection designed to stabilize proteins uncovers a chaperone called Spy.

Quan, S.Koldewey, P.Tapley, T.Kirsch, N.Ruane, K.M.Pfizenmaier, J.Shi, R.Hofmann, S.Foit, L.Ren, G.Jakob, U.Xu, Z.Cygler, M.Bardwell, J.C.

(2011) Nat.Struct.Mol.Biol. 18: 262-269

  • DOI: 10.1038/nsmb.2016

  • PubMed Abstract: 
  • To optimize the in vivo folding of proteins, we linked protein stability to antibiotic resistance, thereby forcing bacteria to effectively fold and stabilize proteins. When we challenged Escherichia coli to stabilize a very unstable periplasmic prote ...

    To optimize the in vivo folding of proteins, we linked protein stability to antibiotic resistance, thereby forcing bacteria to effectively fold and stabilize proteins. When we challenged Escherichia coli to stabilize a very unstable periplasmic protein, it massively overproduced a periplasmic protein called Spy, which increases the steady-state levels of a set of unstable protein mutants up to 700-fold. In vitro studies demonstrate that the Spy protein is an effective ATP-independent chaperone that suppresses protein aggregation and aids protein refolding. Our strategy opens up new routes for chaperone discovery and the custom tailoring of the in vivo folding environment. Spy forms thin, apparently flexible cradle-shaped dimers. The structure of Spy is unlike that of any previously solved chaperone, making it the prototypical member of a new class of small chaperones that facilitate protein refolding in the absence of energy cofactors.


    Organizational Affiliation

    Howard Hughes Medical Institute, Chevy Chase, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic protein related to spheroblast formation
A, B
108Escherichia coli O157:H7Mutation(s): 0 
Gene Names: spy
Find proteins for Q8XDZ4 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8XDZ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.599 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.243 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 68.971α = 90.00
b = 68.971β = 90.00
c = 124.281γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
RESOLVEphasing
REFMACrefinement
SHARPphasing
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description