ClpA Disengaged State bound to RepA-GFP (Focused Classification)

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis.

Lopez, K.E.Rizo, A.N.Tse, E.Lin, J.Scull, N.W.Thwin, A.C.Lucius, A.L.Shorter, J.Southworth, D.R.

(2020) Nat Struct Mol Biol 27: 406-416

  • DOI: https://doi.org/10.1038/s41594-020-0409-5
  • Primary Citation of Related Structures:  
    6UQE, 6UQO, 6W1Z, 6W20, 6W21, 6W22, 6W23, 6W24

  • PubMed Abstract: 

    The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis. A spiral of pore loop-substrate contacts spans both ClpA AAA+ domains. Protomers at the spiral seam undergo nucleotide-specific rearrangements, supporting substrate translocation. IGL loops extend flexibly to bind the planar, heptameric ClpP surface with the empty, symmetry-mismatched IGL pocket maintained at the seam. Three different structures identify a binding-pocket switch by the IGL loop of the lowest positioned protomer, involving release and re-engagement with the clockwise pocket. This switch is coupled to a ClpA rotation and a network of conformational changes across the seam, suggesting that ClpA can rotate around the ClpP apical surface during processive steps of translocation and proteolysis.

  • Organizational Affiliation

    Graduate Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpA
A, B, C, D, E
A, B, C, D, E, F
758Escherichia coli K-12Mutation(s): 0 
Gene Names: clpAlopDb0882JW0866
Find proteins for P0ABH9 (Escherichia coli (strain K12))
Explore P0ABH9 
Go to UniProtKB:  P0ABH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABH9
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RepA, green fluorescent protein fusionG [auth X]24synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
L [auth C]
M [auth C]
N [auth D]
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth E],
Q [auth E]
C10 H16 N5 O13 P3
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
R [auth F]
C10 H15 N5 O10 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-05-27
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references