Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - A7B6C1 Local Symmetry: Cyclic - C7  (3D View)
Local Stoichiometry: Homo 7-mer - A7 

Local Symmetry: Cyclic - C7  (3D View)
Local Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 405.58 kDa 
• Atom Count: 26,527 
• Modelled Residue Count: 3,419 
• Deposited Residue Count: 3,675 
• Unique protein chains: 3

 6PO1

ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4

• PDB DOI:  https://doi.org/10.2210/pdb6PO1/pdb
• EM Map EMD-20406: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-03 Released: 2020-03-11 
• Deposition Author(s): Fei, X., Jenni, S., Harrison, S.C., Sauer, R.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

• PubMed: 32108573 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpX	A, B, C, D, E, F	369	Escherichia coli	Mutation(s): 1  Gene Names: clpX, BUE81_06555
UniProt
Find proteins for P0A6H1 (Escherichia coli (strain K12)) Explore P0A6H1  Go to UniProtKB:  P0A6H1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	207	Escherichia coli	Mutation(s): 0  Gene Names: clpP, A1WS_00920 EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7  Go to UniProtKB:  P0A6G7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
substrate peptide	N [auth S]	12	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	O [auth A], P [auth B], Q [auth C], R [auth D], S [auth E]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP	T [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Fei, X., Jenni, S., Harrison, S.C., Sauer, R.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-101988
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release