ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3

Experimental Data Snapshot

  • Resolution: 4.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.

Fei, X.Bell, T.A.Jenni, S.Stinson, B.M.Baker, T.A.Harrison, S.C.Sauer, R.T.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.52774
  • Primary Citation of Related Structures:  
    6PO1, 6PO3, 6POD, 6POS, 6PP5, 6PP6, 6PP7, 6PP8, 6PPE

  • PubMed Abstract: 

    ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.

  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpX
A, B, C, D, E
A, B, C, D, E, F
369Escherichia coliMutation(s): 1 
Gene Names: clpXBUE81_06555
Find proteins for P0A6H1 (Escherichia coli (strain K12))
Explore P0A6H1 
Go to UniProtKB:  P0A6H1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6H1
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
substrate peptideG [auth S]7Escherichia coliMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 4.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-101988
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Refinement description