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- PDB-9jvp: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bo... -

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Basic information

Entry
Database: PDB / ID: 9jvp
TitleCryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 3
Components
  • (ATP-dependent Clp protease proteolytic subunit ...) x 2
  • ATP-dependent Clp protease ATP-binding subunit ClpC1
  • Beta-casein
KeywordsHYDROLASE / Mycobacterium tuberculosis / Caseinolytic protease system / Activation
Function / homology
Function and homology information


response to 11-deoxycorticosterone / response to dehydroepiandrosterone / negative regulation of lactation / potassium channel inhibitor activity / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / antioxidant activity / protein quality control for misfolded or incompletely synthesized proteins / cysteine-type endopeptidase inhibitor activity ...response to 11-deoxycorticosterone / response to dehydroepiandrosterone / negative regulation of lactation / potassium channel inhibitor activity / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / antioxidant activity / protein quality control for misfolded or incompletely synthesized proteins / cysteine-type endopeptidase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / protein folding chaperone / response to progesterone / peptidoglycan-based cell wall / Golgi lumen / regulation of blood pressure / negative regulation of inflammatory response / response to estradiol / ATPase binding / response to heat / serine-type endopeptidase activity / Golgi apparatus / protein homodimerization activity / ATP hydrolysis activity / extracellular space / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Casein, beta / Casein, alpha/beta / Casein / Casein alpha/beta, conserved site / Caseins alpha/beta signature. / UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain ...Casein, beta / Casein, alpha/beta / Casein / Casein alpha/beta, conserved site / Caseins alpha/beta signature. / UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / ClpP, Ser active site / : / Endopeptidase Clp serine active site. / Clp, repeat (R) domain / Clp repeat (R) domain profile. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / Clp, N-terminal domain superfamily / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ClpP/crotonase-like domain superfamily / ATPase family associated with various cellular activities (AAA) / 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 / Beta-casein / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1 / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Bos grunniens (domestic yak)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsZhou, B. / Zhao, H. / Gao, Y. / Chen, X. / Zhang, T. / He, J. / Xiong, X.
Funding support China, 9items
OrganizationGrant numberCountry
Other government2021YFA1300903
Other government2021YFA1300903
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
DepositionOct 9, 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 ClpC1
B: ATP-dependent Clp protease ATP-binding subunit ClpC1
C: ATP-dependent Clp protease ATP-binding subunit ClpC1
D: ATP-dependent Clp protease ATP-binding subunit ClpC1
E: ATP-dependent Clp protease ATP-binding subunit ClpC1
F: ATP-dependent Clp protease ATP-binding subunit ClpC1
M: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
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
T: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
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
U: Beta-casein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)727,74655
Polymers716,40621
Non-polymers11,34034
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

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

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


Mass: 19782.576 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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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFU

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC1


Mass: 73270.336 Da / Num. of mol.: 6 / Mutation: E288A, F444S, E626A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: clpC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC9
#4: Protein/peptide Beta-casein


Mass: 2624.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos grunniens (domestic yak) / References: UniProt: P02666

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Non-polymers , 4 types, 34 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#8: 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 / Comment: medication*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 ClpC1P1P2 complex bound to bortezomib, conformation 3
Type: COMPLEX / Entity ID: #1-#4 / 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: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 520973 / Symmetry type: POINT

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