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- PDB-8yd0: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bor... -

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Basic information

Entry
Database: PDB / ID: 8yd0
TitleCryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
Components
  • (ATP-dependent Clp protease proteolytic subunit ...) x 2
  • ATP-dependent Clp protease ATP-binding subunit ClpX
KeywordsHYDROLASE / Mycobacterium tuberculosis / Caseinolytic protease system / Activation
Function / homology
Function and homology information


negative regulation of protein polymerization / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone / unfolded protein binding ...negative regulation of protein polymerization / HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone / unfolded protein binding / ATPase binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / zinc ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / : / ClpP, Ser active site / Endopeptidase Clp serine active site. ...Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / : / 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 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ClpP/crotonase-like domain superfamily / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Chem-BO2 / ATP-dependent Clp protease ATP-binding subunit ClpX / 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: 2.24 Å
AuthorsZhou, B. / Zhao, H. / Gao, Y. / Chen, X. / Zhang, T. / He, J. / 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. / Zhao, H. / Gao, Y. / Chen, X. / Zhang, T. / He, J. / Xiong, X.
History
DepositionFeb 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
C: ATP-dependent Clp protease ATP-binding subunit ClpX
D: ATP-dependent Clp protease ATP-binding subunit ClpX
E: ATP-dependent Clp protease ATP-binding subunit ClpX
F: ATP-dependent Clp protease ATP-binding subunit ClpX
H: ATP-dependent Clp protease proteolytic subunit 2
I: 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
O: ATP-dependent Clp protease proteolytic subunit 1
P: ATP-dependent Clp protease proteolytic subunit 1
Q: ATP-dependent Clp protease proteolytic subunit 1
R: ATP-dependent Clp protease proteolytic subunit 1
S: ATP-dependent Clp protease proteolytic subunit 1
T: ATP-dependent Clp protease proteolytic subunit 1
U: ATP-dependent Clp protease proteolytic subunit 1
V: ATP-dependent Clp protease proteolytic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)529,14442
Polymers520,83320
Non-polymers8,31122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpX


Mass: 39057.750 Da / Num. of mol.: 6 / Mutation: E187Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: clpX / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPB9

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ATP-dependent Clp protease proteolytic subunit ... , 2 types, 14 molecules HIKLMNVOPQRSTU

#2: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 21543.566 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
#3: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 19383.111 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: clpP1, clpP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC5, endopeptidase Clp

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Non-polymers , 4 types, 22 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


Mass: 384.237 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM

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Details

Has ligand of interestY
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: CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 380684 / Symmetry type: POINT

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