6BBA

Crystal structure of human mitochondrial ClpP complex with acyldepsipeptide ADEP-28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death.

Wong, K.S.Mabanglo, M.F.Seraphim, T.V.Mollica, A.Mao, Y.Q.Rizzolo, K.Leung, E.Moutaoufik, M.T.Hoell, L.Phanse, S.Goodreid, J.Barbosa, L.R.S.Ramos, C.H.I.Babu, M.Mennella, V.Batey, R.A.Schimmer, A.D.Houry, W.A.

(2018) Cell Chem Biol 25: 1017-1030.e9

  • DOI: https://doi.org/10.1016/j.chembiol.2018.05.014
  • Primary Citation of Related Structures:  
    6BBA

  • PubMed Abstract: 

    Acyldepsipeptides (ADEPs) are potential antibiotics that dysregulate the activity of the highly conserved tetradecameric bacterial ClpP protease, leading to bacterial cell death. Here, we identified ADEP analogs that are potent dysregulators of the human mitochondrial ClpP (HsClpP). These ADEPs interact tightly with HsClpP, causing the protease to non-specifically degrade model substrates. Dysregulation of HsClpP activity by ADEP was found to induce cytotoxic effects via activation of the intrinsic, caspase-dependent apoptosis. ADEP-HsClpP co-crystal structure was solved for one of the analogs revealing a highly complementary binding interface formed by two HsClpP neighboring subunits but, unexpectedly, with HsClpP in the compact conformation. Given that HsClpP is highly expressed in multiple cancers and has important roles in cell metastasis, our findings suggest a therapeutic potential for ADEPs in cancer treatment.


  • Organizational Affiliation

    Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G
221Homo sapiensMutation(s): 0 
Gene Names: CLPP
EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens)
Explore Q16740 
Go to UniProtKB:  Q16740
PHAROS:  Q16740
GTEx:  ENSG00000125656 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16740
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyldepsipeptide ADEP-28
H, I, J, K, L
H, I, J, K, L, M, N
7synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALO
Query on ALO
H, I, J, K, L
H, I, J, K, L, M, N
L-PEPTIDE LINKINGC4 H9 N O3THR
WFP
Query on WFP
H, I, J, K, L
H, I, J, K, L, M, N
L-PEPTIDE LINKINGC9 H9 F2 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.399α = 90
b = 172.399β = 90
c = 135.963γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations