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- PDB-8yd4: CryoEM structure of apo M. tuberculosis ClpP1P2 -

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Basic information

Entry
Database: PDB / ID: 8yd4
TitleCryoEM structure of apo M. tuberculosis ClpP1P2
Components
  • ATP-dependent Clp protease proteolytic subunit 1
  • ATP-dependent Clp protease proteolytic subunit 2
KeywordsHYDROLASE / Mycobacterium tuberculosis / caseinolytic protease system / holoenzymes / antibiotics / Bortezomib
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytosol
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 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsZhou, B. / Gao, Y. / Zhao, H. / Chen, X. / He, J. / Zhang, T. / Xiong, X.
Funding support China, 9items
OrganizationGrant numberCountry
Other government2021YFA1300903
Other government2021YFA1300904
National Natural Science Foundation of China (NSFC)32300152 China
National Natural Science Foundation of China (NSFC)81973372 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)32241021 China
National Natural Science Foundation of China (NSFC)82341085 China
Other government2022A1515110505
Other government2022M723164
CitationJournal: To Be Published
Title: Activation mechanism of caseinolytic chaperone-protease system in Mycobacterium tuberculosis by the anti-cancer drug bortezomib
Authors: Zhou, B. / Gao, Y. / Zhao, H. / Chen, X. / He, J. / Zhang, T. / Xiong, X.
History
DepositionFeb 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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 1
B: ATP-dependent Clp protease proteolytic subunit 1
C: ATP-dependent Clp protease proteolytic subunit 1
D: ATP-dependent Clp protease proteolytic subunit 1
E: ATP-dependent Clp protease proteolytic subunit 1
F: ATP-dependent Clp protease proteolytic subunit 1
G: ATP-dependent Clp protease proteolytic subunit 1
H: ATP-dependent Clp protease proteolytic subunit 2
I: ATP-dependent Clp protease proteolytic subunit 2
J: ATP-dependent Clp protease proteolytic subunit 2
K: ATP-dependent Clp protease proteolytic subunit 2
L: ATP-dependent Clp protease proteolytic subunit 2
M: ATP-dependent Clp protease proteolytic subunit 2
N: ATP-dependent Clp protease proteolytic subunit 2


Theoretical massNumber of molelcules
Total (without water)317,03314
Polymers317,03314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 21727.664 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: clpP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC5, endopeptidase Clp
#2: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 23562.754 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: clpP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC3, endopeptidase Clp
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycobacterium tuberculosis caseinolytic protease P1P2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256622 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00119110
ELECTRON MICROSCOPYf_angle_d0.33925837
ELECTRON MICROSCOPYf_dihedral_angle_d9.5782681
ELECTRON MICROSCOPYf_chiral_restr0.0373003
ELECTRON MICROSCOPYf_plane_restr0.0023367

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