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- PDB-9mk2: Crystal structure of Neisseria meningitidis ClpP protease complex... -

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Basic information

Entry
Database: PDB / ID: 9mk2
TitleCrystal structure of Neisseria meningitidis ClpP protease complex with noncovalent activator, ACP1-01
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / noncovalent / activator / agonist / allosteric
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
: / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,38814
Polymers171,8847
Non-polymers3,5037
Water6,936385
1
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,77528
Polymers343,76814
Non-polymers7,00714
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area64710 Å2
ΔGint-253 kcal/mol
Surface area88280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.350, 118.700, 127.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11E-454-

HOH

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Components

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


Mass: 24554.881 Da / Num. of mol.: 7
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-A1BLZ / 2-methyl-N-(2-{[2-(trifluoromethyl)phenyl]sulfanyl}ethyl)-2-[5-(trifluoromethyl)pyridine-2-sulfonyl]propanamide


Mass: 500.478 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C19H18F6N2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 295 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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→75.27 Å / Num. obs: 107571 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5228 / CC1/2: 0.684 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→75.27 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2386 --
Rwork0.1939 --
obs-107481 100 %
Refinement stepCycle: LAST / Resolution: 1.95→75.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9855 0 224 385 10464
LS refinement shellHighest resolution: 1.95 Å
RfactorNum. reflection
Rfree0.3025 -
Rwork0.2681 -
obs-3495

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