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- EMDB-39157: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-39157
TitleCryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 2
Map data
Sample
  • Complex: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 2
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC1
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
    • Protein or peptide: Beta-casein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
KeywordsMycobacterium tuberculosis / Caseinolytic protease system / Activation / HYDROLASE
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein folding chaperone / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / protein homodimerization activity / ATP hydrolysis activity ...endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein folding chaperone / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / protein homodimerization activity / ATP hydrolysis activity / extracellular space / ATP 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. / Clp, N-terminal domain superfamily / 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 / 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
ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1 / ATP-dependent Clp protease ATP-binding subunit ClpC1 / Beta-casein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria) / Bos grunniens (domestic yak)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsZhou B / Zhao H / Gao Y / Chen X / Zhang T / He J / Xiong X
Funding support China, 9 items
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
DepositionFeb 18, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39157.png

Downloads & links

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Map

FileDownload / File: emd_39157.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 512 pix.
= 363.52 Å		0.71 Å/pix.
x 512 pix.
= 363.52 Å		0.71 Å/pix.
x 512 pix.
= 363.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.05501935 - 0.6993754
Average (Standard dev.)0.0014940879 (±0.015047483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 363.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39157_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39157_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39157_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bo...

EntireName: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 2
Components
  • Complex: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 2
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC1
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
    • Protein or peptide: Beta-casein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE

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Supramolecule #1: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bo...

SupramoleculeName: CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 73.270336 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SLVLDQFGRN LTAAAMEGKL DPVIGREKEI ERVMQVLSRR TKNNPVLIGE PGVGKTAVVE GLAQAIVHGE VPETLKDKQL YTLDLGSLV AGSRYRGDFE ERLKKVLKEI NTRGDIILFI DALHTLVGAG AAEGAIDAAS ILKPKLARGE LQTIGATTLD E YRKYIEKD ...String:
SLVLDQFGRN LTAAAMEGKL DPVIGREKEI ERVMQVLSRR TKNNPVLIGE PGVGKTAVVE GLAQAIVHGE VPETLKDKQL YTLDLGSLV AGSRYRGDFE ERLKKVLKEI NTRGDIILFI DALHTLVGAG AAEGAIDAAS ILKPKLARGE LQTIGATTLD E YRKYIEKD AALERRFQPV QVGEPTVEHT IEILKGLRDR YEAHHRVSIT DAAMVAAATL ADRYINDRFL PDKAIDLIDE AG ARMRIRR MTAPPDLREF DEKIAEARRE KESAIDAQDS EKAASLRDRE KTLVAQRAER EKQWRSGDLD VVAEVDDEQI AEV LGNWTG IPVFKLTEAE TTRLLRMEEE LHKRIIGQED AVKAVSKAIR RTRAGLKDPK RPSGSFIFAG PSGVGKTELS KALA NFLFG DDDALIQIDM GEFHDRFTAS RLFGAPPGYV GYEEGGQLTE KVRRKPFSVV LFDAIEKAHQ EIYNSLLQVL EDGRL TDGQ GRTVDFKNTV LIFTSNLGTS DISKPVGLGF SKGGGENDYE RMKQKVNDEL KKHFRPEFLN RIDDIIVFHQ LTREEI IRM VDLMISRVAG QLKSKDMALV LTDAAKALLA KRGFDPVLGA RPLRRTIQRE IEDQLSEKIL FEEVGPGQVV TVDVDNW DG EGPGEDAVFT FTGTR

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpC1

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Macromolecule #2: ATP-dependent Clp protease proteolytic subunit 2

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 21.43041 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LPSFIEHSSF GVKESNPYNK LFEERIIFLG VQVDDASAND IMAQLLVLES LDPDRDITMY INSPGGGFTS LMAIYDTMQY VRADIQTVC LGQAASAAAV LLAAGTPGKR MALPNARVLI HQPSLSGVIQ GQFSDLEIQA AEIERMRTLM ETTLARHTGK D AGVIRKDT ...String:
LPSFIEHSSF GVKESNPYNK LFEERIIFLG VQVDDASAND IMAQLLVLES LDPDRDITMY INSPGGGFTS LMAIYDTMQY VRADIQTVC LGQAASAAAV LLAAGTPGKR MALPNARVLI HQPSLSGVIQ GQFSDLEIQA AEIERMRTLM ETTLARHTGK D AGVIRKDT DRDKILTAEE AKDYGIIDTV LEYRKLS

UniProtKB: ATP-dependent Clp protease proteolytic subunit 2

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Macromolecule #3: ATP-dependent Clp protease proteolytic subunit 1

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 19.383111 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SLTDSVYERL LSERIIFLGS EVNDEIANRL CAQILLLAAE DASKDISLYI NSPGGSISAG MAIYDTMVLA PCDIATYAMG MAASMGEFL LAAGTKGKRY ALPHARILMH QPLGGVTGSA ADIAIQAEQF AVIKKEMFRL NAEFTGQPIE RIEADSDRDR W FTAAEALE YGFVDHIITR

UniProtKB: ATP-dependent Clp protease proteolytic subunit 1

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Macromolecule #4: Beta-casein

MacromoleculeName: Beta-casein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos grunniens (domestic yak)
Molecular weightTheoretical: 2.493056 KDa
SequenceString:
KVLILACLVA LALARELEEL NVP

UniProtKB: Beta-casein

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL...

MacromoleculeName: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
type: ligand / ID: 8 / Number of copies: 14 / Formula: BO2
Molecular weightTheoretical: 384.237 Da
Chemical component information

ChemComp-BO2:
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vgq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 433061
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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