4D2Q | pdb_00004d2q

Negative-stain electron microscopy of E. coli ClpB mutant E432A (BAP form bound to ClpP)

• PDB DOI: https://doi.org/10.2210/pdb4D2Q/pdb
• EM Map EMD-2555: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-12 Released: 2014-06-04 
• Deposition Author(s): Carroni, M., Kummer, E., Oguchi, Y., Clare, D.K., Wendler, P., Sinning, I., Kopp, J., Mogk, A., Bukau, B., Saibil, H.R.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 18.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Head-to-Tail Interactions of the Coiled-Coil Domains Regulate Clpb Activity and 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.R.

(2014) Elife 3: 02481

• PubMed: 24843029 
• 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.
Zentrum für Molekulare Biologie, Universität Heidelberg, Heidelberg, Germany.
Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany.
Biochemie-Zentrum, Universität Heidelberg, Heidelberg, Germany.
Department of Crystallography, Birkbeck College, University of London, London, United Kingdom [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 581.01 kDa 
• Atom Count: 14,201 
• Modeled Residue Count: 4,734 
• Deposited Residue Count: 5,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLPB	A, B, C, D, E, F	858	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P63284 (Escherichia coli (strain K12)) Explore P63284  Go to UniProtKB:  P63284

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 18.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Carroni, M., Kummer, E., Oguchi, Y., Clare, D.K., Wendler, P., Sinning, I., Kopp, J., Mogk, A., Bukau, B., Saibil, H.R.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Other
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary