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- PDB-6bba: Crystal structure of human mitochondrial ClpP complex with acylde... -

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Basic information

Entry
Database: PDB / ID: 6bba
TitleCrystal structure of human mitochondrial ClpP complex with acyldepsipeptide ADEP-28
Components
  • ATP-dependent Clp protease proteolytic subunit, mitochondrial
  • Acyldepsipeptide ADEP-28
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protease / proteostasis / protein quality control / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix ...membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Cell Chem Biol / Year: 2018
Title: Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death.
Authors: 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. ...Authors: 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.
History
DepositionOct 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
H: Acyldepsipeptide ADEP-28
I: Acyldepsipeptide ADEP-28
J: Acyldepsipeptide ADEP-28
K: Acyldepsipeptide ADEP-28
L: Acyldepsipeptide ADEP-28
M: Acyldepsipeptide ADEP-28
N: Acyldepsipeptide ADEP-28


Theoretical massNumber of molelcules
Total (without water)174,89414
Polymers174,89414
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, assembly also confirmed by SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31870 Å2
ΔGint-95 kcal/mol
Surface area51320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.399, 172.399, 135.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit, mitochondrial / Endopeptidase Clp


Mass: 24179.875 Da / Num. of mol.: 7 / Fragment: residues 58-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q16740, endopeptidase Clp
#2: Protein/peptide
Acyldepsipeptide ADEP-28


Mass: 804.920 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate pH 4.6, 4% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.796→50 Å / Num. obs: 57827 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.056 / Rrim(I) all: 0.188 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2896 / Rpim(I) all: 0.566 / Rrim(I) all: 0.188 / Χ2: 0.684 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TG6

1tg6


Resolution: 2.796→46.735 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2017 3.49 %
Rwork0.1866 --
obs0.1883 57827 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.796→46.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10233 0 392 208 10833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910856
X-RAY DIFFRACTIONf_angle_d1.18114718
X-RAY DIFFRACTIONf_dihedral_angle_d24.9044094
X-RAY DIFFRACTIONf_chiral_restr0.0621686
X-RAY DIFFRACTIONf_plane_restr0.0071860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7956-2.86550.34711430.30733892X-RAY DIFFRACTION99
2.8655-2.9430.32451410.2713956X-RAY DIFFRACTION100
2.943-3.02950.32041410.23673961X-RAY DIFFRACTION100
3.0295-3.12730.28131430.2343967X-RAY DIFFRACTION100
3.1273-3.23910.33291450.22813958X-RAY DIFFRACTION100
3.2391-3.36870.31421420.23083953X-RAY DIFFRACTION100
3.3687-3.5220.27971450.21063961X-RAY DIFFRACTION100
3.522-3.70760.2591420.18043982X-RAY DIFFRACTION100
3.7076-3.93980.20721430.17193985X-RAY DIFFRACTION100
3.9398-4.24380.18751440.15563998X-RAY DIFFRACTION100
4.2438-4.67050.19751480.14574014X-RAY DIFFRACTION100
4.6705-5.34550.20541450.15994001X-RAY DIFFRACTION100
5.3455-6.73160.23791450.19164054X-RAY DIFFRACTION100
6.7316-46.74140.19451500.1754128X-RAY DIFFRACTION99

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