4F00

Crystal structure of the substrate binding domain of E.coli DnaK in complex with an apidaecin fragment from the bumblebee (residues 3 to 11)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


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


Literature

Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK.

Zahn, M., Berthold, N., Kieslich, B., Knappe, D., Hoffmann, R., Strater, N.

(2013) J Mol Biol 425: 2463-2479

  • DOI: 10.1016/j.jmb.2013.03.041
  • Primary Citation of Related Structures:  
    4EZN, 4EZO, 4EZP, 4EZQ, 4EZR, 4EZT, 4EZW, 4EZX, 4EZY, 4EZZ, 4F00, 4F01, 4HY9, 4HYB

  • PubMed Abstract: 

    • Hsp70 chaperones have been implicated in assisting protein folding of newly synthesized polypeptide chains, refolding of misfolded proteins, and protein trafficking. For these functions, the chaperones need to exhibit a significant promiscuity in binding to different sequences of hydrophobic peptide stretches ...

    Hsp70 chaperones have been implicated in assisting protein folding of newly synthesized polypeptide chains, refolding of misfolded proteins, and protein trafficking. For these functions, the chaperones need to exhibit a significant promiscuity in binding to different sequences of hydrophobic peptide stretches. To characterize the structural basis of sequence specificity and flexibility of the Escherichia coli Hsp70 chaperone DnaK, we have analyzed crystal structures of the substrate binding domain of the protein in complex with artificially designed peptides as well as small proline-rich antimicrobial peptides. The latter peptides from mammals and insects were identified to target DnaK after cell penetration. Interestingly, the complex crystal structures reveal two different peptide binding modes. The peptides can bind either in a forward or in a reverse direction to the conventional substrate binding cleft of DnaK in an extended conformation. Superposition of the two binding modes shows a remarkable similarity in the side chain orientations and hydrogen bonding pattern despite the reversed peptide orientation. The DnaK chaperone has evolved to bind peptides in both orientations in the substrate binding cleft with comparable energy without rearrangements of the protein. Optimal hydrophobic interactions with binding pockets -2 to 0 appear to be the main determinant for the orientation and sequence position of peptide binding.

    Organizational Affiliation: 

    Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chaperone protein DnaKA219Escherichia coli K-12Mutation(s): 0 
Gene Names: b0014, dnaK, groP, grpF, JW0013, seg
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Explore P0A6Y8 
Go to UniProtKB:  P0A6Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6Y8
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ApidaecinB10Bombus pascuorumMutation(s): 0 
UniProt
Find proteins for P81464 (Bombus pascuorum)
Explore P81464 
Go to UniProtKB:  P81464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81464
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.156α = 90
b = 116.201β = 90
c = 37.169γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-05-03 
  • Released Date: 2013-04-17 
    • Deposition Author(s): Zahn, M., Straeter, N.

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description