8W1M | pdb_00008w1m

T.thermophilus DNAK nucleotide binding domain in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.259 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mechanisms of assembly and function of the Hsp70-Hsp40 chaperone machinery.

Jiang, Y.Ibrahim, Z.Xia, Y.Clay, M.Myasnikov, A.Immadisetty, K.Xia, Z.Tang, L.Rossi, P.Ganguly, P.Liu, J.Miller, D.Che, M.Palacios, S.M.Kramer, G.Bukau, B.Kalodimos, C.G.

(2025) Mol Cell 85: 4032-4046.e7

  • DOI: https://doi.org/10.1016/j.molcel.2025.09.023
  • Primary Citation of Related Structures:  
    8W1M, 9DYU, 9DYV

  • PubMed Abstract: 

    Hsp70 and Hsp40 molecular chaperones form a central machinery that remodels client proteins involved in numerous biological processes. Here, we integrated cryo-electron microscopy and nuclear magnetic resonance spectroscopy to determine the architecture of the full-length Hsp70-Hsp40 machinery. The structure of the complex in a physiologically inhibited state reveals distinct regulatory mechanisms. In the active state, the Hsp40 glycine-phenylalanine (G/F)-rich region acts as a pseudo-substrate for Hsp70, directly modulating refolding. This region also maintains Hsp40 in an autoinhibited state; upon binding to Hsp70, the inhibition is disrupted, exposing a cryptic client-binding site that enables client engagement and refolding. Transitions between these states are central to controlling refolding efficiency. Disrupting either the autoinhibited state or the G/F-Hsp70 interaction impairs function and elicits a compensatory heat shock response in cells. Our findings uncover the regulatory dynamics of a fundamental chaperone system, with broad implications for understanding protein homeostasis and the cellular response to stress.


  • Organizational Affiliation
    • State Key Laboratory of Pharmaceutical Biotechnology, Department of Oncology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DnaK
A, B
382Thermus thermophilusMutation(s): 0 
Gene Names: dnaKTTHA1491
UniProt
Find proteins for Q56235 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56235 
Go to UniProtKB:  Q56235
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56235
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.259 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.761α = 90
b = 179.939β = 90
c = 66.587γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
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 StatesR35 GM122462

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references