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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wwPDB Validation 3D Report Full Report

Validation slider image for 8W1M

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 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.

Macromolecule Content 

  • Total Structure Weight: 83.62 kDa 
  • Atom Count: 5,779 
  • Modeled Residue Count: 760 
  • Deposited Residue Count: 764 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

View Full Validation Report



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