6VFS

ClpXP from Neisseria meningitidis - Conformation A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery.

Ripstein, Z.A.Vahidi, S.Houry, W.A.Rubinstein, J.L.Kay, L.E.

(2020) Elife 9: --

  • DOI: 10.7554/eLife.52158
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development ag ...

    The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development against infectious diseases. Although structures are available for isolated ClpX and ClpP rings, it remains unknown how symmetry mismatched ClpX and ClpP work in tandem for processive substrate translocation into the ClpP proteolytic chamber. Here we present cryo-EM structures of the substrate-bound ClpXP complex from Neisseria meningitidis at 2.3 to 3.3 Å resolution. The structures allow development of a model in which the sequential hydrolysis of ATP is coupled to motions of ClpX loops that lead to directional substrate translocation and ClpX rotation relative to ClpP. Our data add to the growing body of evidence that AAA+ molecular machines generate translocating forces by a common mechanism.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease ATP-binding subunit ClpX
E, A, F, C, B, D
414Neisseria meningitidisMutation(s): 0 
Gene Names: clpX
Find proteins for A0A0Y4ZJG4 (Neisseria meningitidis)
Go to UniProtKB:  A0A0Y4ZJG4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Unidentified protein substrate
G
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
L, O, P, Q, R, S, T, U, H, I, J, K, M, N
204Neisseria meningitidisMutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
Find proteins for A0A0Y5K536 (Neisseria meningitidis)
Go to UniProtKB:  A0A0Y5K536
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B, C, D, E
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN-503573
Canadian Institutes of Health Research (CIHR)CanadaPJT-162186
Canadian Institutes of Health Research (CIHR)CanadaPJT-148564

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release