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- PDB-9mjp: Crystal structure of Neisseria meningitidis ClpP protease complex... -

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Basic information

Entry
Database: PDB / ID: 9mjp
TitleCrystal structure of Neisseria meningitidis ClpP protease complex with boronate compound BC8a
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / boronate / covalent / inhibitor / activator
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Chem-JT7 / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Structure / Year: 2025
Title: Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways.
Authors: Barghash, M.M. / Mabanglo, M.F. / Hoff, S.E. / Brozdnychenko, D. / Wong, K.S. / Binepal, G. / Ip, P. / Shen, J. / Furukawa, T. / Katayama, H. / Trudel, V. / Tan, J. / Yudin, A.K. / Gray- ...Authors: Barghash, M.M. / Mabanglo, M.F. / Hoff, S.E. / Brozdnychenko, D. / Wong, K.S. / Binepal, G. / Ip, P. / Shen, J. / Furukawa, T. / Katayama, H. / Trudel, V. / Tan, J. / Yudin, A.K. / Gray-Owen, S.D. / Sakuda, S. / Batey, R.A. / Vahidi, S. / Bonomi, M. / Houry, W.A.
History
DepositionDec 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,54628
Polymers343,76814
Non-polymers5,77814
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48270 Å2
ΔGint-163 kcal/mol
Surface area90330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.122, 127.548, 119.387
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 24554.881 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP, NMB1312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JZ38, endopeptidase Clp
#2: Chemical
ChemComp-JT7 / N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide


Mass: 412.716 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C19H30BClN2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 41.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium thiocyanate or potassium acetate, pH 7.5, 40% (+/-)-2-methyl-2,4-pentanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18061 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18061 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 1.99→48.68 Å / Num. obs: 183449 / % possible obs: 92.5 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 28.6
Reflection shellResolution: 1.99→2.04 Å / % possible obs: 70.4 % / Num. unique obs: 9997 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.68 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2336 --
Rwork0.1951 --
obs-183449 92.5 %
Refinement stepCycle: LAST / Resolution: 1.99→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19668 0 0 281 19949
LS refinement shellHighest resolution: 1.99 Å
RfactorNum. reflection
Rfree0.3234 -
Rwork0.3014 -
obs-9997

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