6OAY | pdb_00006oay

Structure of the hyperactive ClpB mutant K476C, bound to casein, post-state

• PDB DOI: https://doi.org/10.2210/pdb6OAY/pdb
• EM Map EMD-20005: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Escherichia coli K-12, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-18 Released: 2019-06-12 
• Deposition Author(s): Rizo, A.R., Lin, J.-B., Gates, S.N., Tse, E., Bart, S.M., Castellano, L.M., Dimaio, F., Shorter, J., Southworth, D.R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase.

Rizo, A.N., Lin, J., Gates, S.N., Tse, E., Bart, S.M., Castellano, L.M., DiMaio, F., Shorter, J., Southworth, D.R.

(2019) Nat Commun 10: 2393-2393

• PubMed: 31160557 
• DOI: https://doi.org/10.1038/s41467-019-10150-y
• Primary Citation Related Structures: 
  6OAX, 6OAY, 6OG1, 6OG2, 6OG3


• PubMed Abstract: 
  

  Bacterial ClpB and yeast Hsp104 are homologous Hsp100 protein disaggregases that serve critical functions in proteostasis by solubilizing protein aggregates. Two AAA+ nucleotide binding domains (NBDs) power polypeptide translocation through a central channel comprised of a hexameric spiral of protomers that contact substrate via conserved pore-loop interactions. Here we report cryo-EM structures of a hyperactive ClpB variant bound to the model substrate, casein in the presence of slowly hydrolysable ATPγS, which reveal the translocation mechanism. Distinct substrate-gripping interactions are identified for NBD1 and NBD2 pore loops. A trimer of N-terminal domains define a channel entrance that binds the polypeptide substrate adjacent to the topmost NBD1 contact. NBD conformations at the seam interface reveal how ATP hydrolysis-driven substrate disengagement and re-binding are precisely tuned to drive a directional, stepwise translocation cycle.

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Organizational Affiliation: 
• Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA.
Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A6B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A4B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 589.71 kDa 
• Atom Count: 27,261 
• Modeled Residue Count: 3,412 
• Deposited Residue Count: 5,228 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyperactive disaggregase ClpB	A [auth C], B [auth F], C [auth E], D, E [auth B], F [auth A]	867	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P63284 (Escherichia coli (strain K12)) Explore P63284  Go to UniProtKB:  P63284

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-S1-casein	G [auth P]	26	Bos taurus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	H [auth C], I [auth C], K [auth E], L [auth E], M [auth D], N [auth D], O [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP	J [auth F], P [auth B], Q [auth A], R [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Rizo, A.R., Lin, J.-B., Gates, S.N., Tse, E., Bart, S.M., Castellano, L.M., Dimaio, F., Shorter, J., Southworth, D.R.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-06-19
  Changes: Data collection, Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2025-05-14
  Changes: Data collection, Structure summary