4CIU | pdb_00004ciu

Crystal structure of E. coli ClpB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4CIU

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Head-to-Tail Interactions of the Coiled-Coil Domains Regulate Clpb Cooperation with Hsp70 in Protein Disaggregation

Carroni, M.Kummer, E.Oguchi, Y.Wendler, P.Clare, D.K.Sinning, I.Kopp, J.Mogk, A.Bukau, B.Saibil, H.

(2014) Elife 3: 02481

  • DOI: https://doi.org/10.7554/eLife.02481
  • Primary Citation Related Structures: 
    4CIU, 4D2Q, 4D2U, 4D2X

  • PubMed Abstract: 

    The hexameric AAA+ chaperone ClpB reactivates aggregated proteins in cooperation with the Hsp70 system. Essential for disaggregation, the ClpB middle domain (MD) is a coiled-coil propeller that binds Hsp70. Although the ClpB subunit structure is known, positioning of the MD in the hexamer and its mechanism of action are unclear. We obtained electron microscopy (EM) structures of the BAP variant of ClpB that binds the protease ClpP, clearly revealing MD density on the surface of the ClpB ring. Mutant analysis and asymmetric reconstructions show that MDs adopt diverse positions in a single ClpB hexamer. Adjacent, horizontally oriented MDs form head-to-tail contacts and repress ClpB activity by preventing Hsp70 interaction. Tilting of the MD breaks this contact, allowing Hsp70 binding, and releasing the contact in adjacent subunits. Our data suggest a wavelike activation of ClpB subunits around the ring.DOI: http://dx.doi.org/10.7554/eLife.02481.001.


  • Organizational Affiliation
    • Department of Crystallography, Birkbeck College, University of London, London, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 83.69 kDa 
  • Atom Count: 5,257 
  • Modeled Residue Count: 657 
  • Deposited Residue Count: 727 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHAPERONE PROTEIN CLPB727Escherichia coliMutation(s): 3 
UniProt
Find proteins for P63284 (Escherichia coli (strain K12))
Explore P63284 
Go to UniProtKB:  P63284
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63284
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.329α = 90
b = 127.329β = 90
c = 119.852γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary