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Structure paper

TitleStructures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.
Journal, issue, pagesElife, Vol. 9, Year 2020
Publish dateFeb 28, 2020
AuthorsXue Fei / Tristan A Bell / Simon Jenni / Benjamin M Stinson / Tania A Baker / Stephen C Harrison / Robert T Sauer /
PubMed AbstractClpXP 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 ...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 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.
External linksElife / PubMed:32108573 / PubMed Central
MethodsEM (single particle)
Resolution3.19 - 4.28 Å
Structure data

20406

6po1

EMDB-20406, PDB-6po1:
ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4
Method: EM (single particle) / Resolution: 4.2 Å

20408

6po3

EMDB-20408, PDB-6po3:
ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3
Method: EM (single particle) / Resolution: 4.28 Å

20412

6pod

EMDB-20412, PDB-6pod:
ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2
Method: EM (single particle) / Resolution: 4.05 Å

20418

6pos

EMDB-20418, PDB-6pos:
ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 1
Method: EM (single particle) / Resolution: 4.12 Å

20419

6pp5

EMDB-20419, PDB-6pp5:
ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4
Method: EM (single particle) / Resolution: 3.98 Å

20420

6pp6

EMDB-20420, PDB-6pp6:
ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3
Method: EM (single particle) / Resolution: 4.28 Å

20421

6pp7

EMDB-20421, PDB-6pp7:
ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2
Method: EM (single particle) / Resolution: 4.05 Å

20422

6pp8

EMDB-20422, PDB-6pp8:
ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 1
Method: EM (single particle) / Resolution: 4.12 Å

20434

6ppe

EMDB-20434, PDB-6ppe:
ClpP and ClpX IGF loop in ClpX-ClpP complex with D7 symmetry
Method: EM (single particle) / Resolution: 3.19 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (E. coli)
KeywordsCHAPERONE / Protein degradation / AAA+ protease complex

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