4J7Z | pdb_00004j7z

Thermus thermophilus DNAJ J- and G/F-DOMAINS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.246 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.214 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 
  • Method: EPR

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ.

Barends, T.R., Brosi, R.W., Steinmetz, A., Scherer, A., Hartmann, E., Eschenbach, J., Lorenz, T., Seidel, R., Shoeman, R.L., Zimmermann, S., Bittl, R., Schlichting, I., Reinstein, J.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1540-1552

  • DOI: https://doi.org/10.1107/S0907444913010640
  • Primary Citation Related Structures: 
    4J7Z, 4J80

  • PubMed Abstract: 

    Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

    • Organizational Affiliation: 
    • MPI for Medical Research, Heidelberg, Germany. thomas.barends@mpimf-heidelberg.mpg.de

Macromolecule Content 

  • Total Structure Weight: 77.8 kDa 
  • Atom Count: 5,278 
  • Modeled Residue Count: 601 
  • Deposited Residue Count: 678 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chaperone protein DnaJ 2
A, B, C, D, E
A, B, C, D, E, F
113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: dnaJ2, TTHA1489
UniProt
Find proteins for Q56237 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56237 
Go to UniProtKB:  Q56237
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56237
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.246 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.214 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
  • Method: EPR
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.99α = 90
b = 85.99β = 90
c = 72.72γ = 120
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations