6SFX

Cryo-EM structure of ClpP1/2 in the LmClpXP1/2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the ClpXP protein degradation machinery.

Gatsogiannis, C.Balogh, D.Merino, F.Sieber, S.A.Raunser, S.

(2019) Nat Struct Mol Biol 26: 946-954

  • DOI: https://doi.org/10.1038/s41594-019-0304-0
  • Primary Citation of Related Structures:  
    6SFW, 6SFX

  • PubMed Abstract: 

    The ClpXP machinery is a two-component protease complex that performs targeted protein degradation in bacteria and mitochondria. The complex consists of the AAA+ chaperone ClpX and the peptidase ClpP. The hexameric ClpX utilizes the energy of ATP binding and hydrolysis to engage, unfold and translocate substrates into the catalytic chamber of tetradecameric ClpP, where they are degraded. Formation of the complex involves a symmetry mismatch, because hexameric AAA+ rings bind axially to the opposing stacked heptameric rings of the tetradecameric ClpP. Here we present the cryo-EM structure of ClpXP from Listeria monocytogenes. We unravel the heptamer-hexamer binding interface and provide novel insight into the ClpX-ClpP cross-talk and activation mechanism. Comparison with available crystal structures of ClpP and ClpX in different states allows us to understand important aspects of the complex mode of action of ClpXP and provides a structural framework for future pharmacological applications.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G
190Listeria monocytogenesMutation(s): 1 
Gene Names: clpPAF298_10370ARH36_13110B1O28_12965B1O52_13110EFC24_09160EHH22_02890EK32_11400JJ01_06855
EC: 3.4.21.92
UniProt
Find proteins for A0A3T2ER33 (Listeria monocytogenes)
Explore A0A3T2ER33 
Go to UniProtKB:  A0A3T2ER33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3T2ER33
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
H, I, J, K, L
H, I, J, K, L, M, N
198Listeria monocytogenesMutation(s): 1 
Gene Names: clpPLmNIHS28_02056
EC: 3.4.21.92
UniProt
Find proteins for Q9RQI6 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q9RQI6 
Go to UniProtKB:  Q9RQI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RQI6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPHIRE1.0
MODEL REFINEMENTRosetta
MODEL REFINEMENTNAMD
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Research CouncilGermany615984
German Research FoundationGermanySFB1035

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references