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- PDB-7wh5: Crystal structure of human ClpP in complex with ZG180 -

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Basic information

Entry
Database: PDB / ID: 7wh5
TitleCrystal structure of human ClpP in complex with ZG180
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / 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
Chem-9DF / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsWei, B.Y. / Gan, J.H. / Yang, C.-G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22037007 China
National Natural Science Foundation of China (NSFC)21725801 China
National Natural Science Foundation of China (NSFC)22107109 China
CitationJournal: Nat Commun / Year: 2022
Title: Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP.
Authors: Wei, B. / Zhang, T. / Wang, P. / Pan, Y. / Li, J. / Chen, W. / Zhang, M. / Ji, Q. / Wu, W. / Lan, L. / Gan, J. / Yang, C.G.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: ATP-dependent Clp protease proteolytic subunit, mitochondrial
I: ATP-dependent Clp protease proteolytic subunit, mitochondrial
J: ATP-dependent Clp protease proteolytic subunit, mitochondrial
K: ATP-dependent Clp protease proteolytic subunit, mitochondrial
L: ATP-dependent Clp protease proteolytic subunit, mitochondrial
M: ATP-dependent Clp protease proteolytic subunit, mitochondrial
N: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,94329
Polymers338,65914
Non-polymers7,28415
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical gel filtration indicatges ClpP as a tetradecamer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50600 Å2
ΔGint-254 kcal/mol
Surface area81270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.890, 97.025, 131.420
Angle α, β, γ (deg.)90.000, 93.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24189.912 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical
ChemComp-9DF / (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide


Mass: 518.571 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C27H33F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→54.38 Å / Num. obs: 156976 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
2.13-2.196.51.2311569761100
9.53-54.386.90.042156976199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TG6

1tg6


Resolution: 2.13→54.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.868 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 7770 5 %RANDOM
Rwork0.23 ---
obs0.2318 148823 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.65 Å2 / Biso mean: 51.405 Å2 / Biso min: 23.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-1.06 Å2
2---2.52 Å20 Å2
3---3.83 Å2
Refinement stepCycle: final / Resolution: 2.13→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18299 0 519 254 19072
Biso mean--75.33 44.66 -
Num. residues----2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01919208
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218092
X-RAY DIFFRACTIONr_angle_refined_deg1.6442.01226112
X-RAY DIFFRACTIONr_angle_other_deg1.008341960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80352357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10224.417686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.307153220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921580
X-RAY DIFFRACTIONr_chiral_restr0.0920.23026
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023471
LS refinement shellResolution: 2.13→2.182 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.401 508 -
Rwork0.381 10627 -
obs--96.12 %

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