4R5J

Crystal structure of the DnaK C-terminus (Dnak-SBD-A)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.361 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural Basis for the Inhibition of HSP70 and DnaK Chaperones by Small-Molecule Targeting of a C-Terminal Allosteric Pocket.

Leu, J.I., Zhang, P., Murphy, M.E., Marmorstein, R., George, D.L.

(2014) Acs Chem.Biol. 9: 2508-2516

  • DOI: 10.1021/cb500236y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The stress-inducible mammalian heat shock protein 70 (HSP70) and its bacterial orthologue DnaK are highly conserved nucleotide binding molecular chaperones. They represent critical regulators of cellular proteostasis, especially during conditions of ...

    The stress-inducible mammalian heat shock protein 70 (HSP70) and its bacterial orthologue DnaK are highly conserved nucleotide binding molecular chaperones. They represent critical regulators of cellular proteostasis, especially during conditions of enhanced stress. Cancer cells rely on HSP70 for survival, and this chaperone represents an attractive new therapeutic target. We have used a structure-activity approach and biophysical methods to characterize a class of inhibitors that bind to a unique allosteric site within the C-terminus of HSP70 and DnaK. Data from X-ray crystallography together with isothermal titration calorimetry, mutagenesis, and cell-based assays indicate that these inhibitors bind to a previously unappreciated allosteric pocket formed within the non-ATP-bound protein state. Moreover, binding of inhibitor alters the local protein conformation, resulting in reduced chaperone-client interactions and impairment of proteostasis. Our findings thereby provide a new chemical scaffold and target platform for both HSP70 and DnaK; these will be important tools with which to interrogate chaperone function and to aid ongoing efforts to optimize potency and efficacy in developing modulators of these chaperones for therapeutic use.

    Organizational Affiliation: 

    Department of Genetics, ‡Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, and §Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperone protein DnaK
A, B, C, D
228Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaK (groP, grpF, seg)
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Y8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.361 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.658α = 102.12
b = 69.412β = 104.20
c = 75.771γ = 92.96
Software Package:
Software NamePurpose
PHASERphasing
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references