7N46

ADP-binding state of the nucleotide-binding domain of Hsp70 DnaK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Conformational equilibria in allosteric control of Hsp70 chaperones.

Wang, W.Liu, Q.Liu, Q.Hendrickson, W.A.

(2021) Mol Cell 81: 3919-3933.e7

  • DOI: https://doi.org/10.1016/j.molcel.2021.07.039
  • Primary Citation of Related Structures:  
    7KO2, 7KRT, 7KRU, 7KRV, 7KRW, 7N46, 7RAX

  • PubMed Abstract: 

    Heat-shock proteins of 70 kDa (Hsp70s) are vital for all life and are notably important in protein folding. Hsp70s use ATP binding and hydrolysis at a nucleotide-binding domain (NBD) to control the binding and release of client polypeptides at a substrate-binding domain (SBD); however, the mechanistic basis for this allostery has been elusive. Here, we first characterize biochemical properties of selected domain-interface mutants in bacterial Hsp70 DnaK. We then develop a theoretical model for allosteric equilibria among Hsp70 conformational states to explain the observations: a restraining state, Hsp70 R -ATP, restricts ATP hydrolysis and binds peptides poorly, whereas a stimulating state, Hsp70 S -ATP, hydrolyzes ATP rapidly and has high intrinsic substrate affinity but rapid binding kinetics. We support this model for allosteric regulation with DnaK structures obtained in the postulated stimulating state S with biochemical tests of the S-state interface and with improved peptide-binding-site definition in an R-state structure.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DnaK386Escherichia coli K-12Mutation(s): 0 
Gene Names: dnaKFAZ83_07380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.646α = 90
b = 101.646β = 90
c = 153.444γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107462

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-07-17
    Changes: Database references