6VFS

ClpXP from Neisseria meningitidis - Conformation A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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:  
    6VFX, 6VFS

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpXA, B, C, D, E, F414Neisseria meningitidisMutation(s): 0 
Gene Names: clpXCOH52_00090COI09_01415ERS514410_00003NCTC8554_00172
Find proteins for Q9JYY3 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JYY3 
Go to UniProtKB:  Q9JYY3
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Unidentified protein substrateG7Escherichia coli BL21(DE3)Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunitH, I, J, K, L, M, N, O, P, Q, R, S, T, U204Neisseria meningitidisMutation(s): 0 
Gene Names: clpPCOI09_01760ERS514410_00057
EC: 3.4.21.92
Find proteins for Q9JZ38 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZ38 
Go to UniProtKB:  Q9JZ38
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download CCD File 
B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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