5OG1

Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.

Deville, C.Carroni, M.Franke, K.B.Topf, M.Bukau, B.Mogk, A.Saibil, H.R.

(2017) Sci Adv 3: e1701726-e1701726

  • DOI: 10.1126/sciadv.1701726
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including <i>Escherichia coli </i> ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through ...

    Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'- O -(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.


    Organizational Affiliation

    Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.,Center for Molecular Biology of the Heidelberg University, German Cancer Research Center, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperone protein ClpB,ATP-dependent Clp protease ATP-binding subunit ClpA,Chaperone protein ClpB
C, F, E, D, B, A
871Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: clpB (htpM), clpA (lopD)
Find proteins for P63284 (Escherichia coli (strain K12))
Go to UniProtKB:  P63284
Find proteins for P0ABH9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABH9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download SDF File 
Download CCD File 
B, C, D, E
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106252
Wellcome TrustUnited Kingdom101488
Wellcome TrustUnited Kingdom079605
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L014211/1
Medical Research Council (United Kingdom)United KingdomMR/M019292/1
German Research FoundationGermanyBB617/17-2
German Research FoundationGermanyMO 970/4-2

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references
  • Version 1.2: 2019-02-20
    Type: Advisory, Data collection, Derived calculations