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- EMDB-39164: CryoEM structure of apo M. tuberculosis ClpP1P2 -

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Basic information

Entry
Database: EMDB / ID: EMD-39164
TitleCryoEM structure of apo M. tuberculosis ClpP1P2
Map data
Sample
  • Complex: Mycobacterium tuberculosis caseinolytic protease P1P2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2
KeywordsMycobacterium tuberculosis / caseinolytic protease system / holoenzymes / antibiotics / Bortezomib / 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 / 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 (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle 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, 9 items
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, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39164.png

Downloads & links

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Map

FileDownload / File: emd_39164.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.1247132 - 1.7316132
Average (Standard dev.)0.00119222 (±0.06277469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 225.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39164_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39164_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39164_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis caseinolytic protease P1P2

EntireName: Mycobacterium tuberculosis caseinolytic protease P1P2
Components
  • Complex: Mycobacterium tuberculosis caseinolytic protease P1P2
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 1
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit 2

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Supramolecule #1: Mycobacterium tuberculosis caseinolytic protease P1P2

SupramoleculeName: Mycobacterium tuberculosis caseinolytic protease P1P2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 21.727664 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSQVTDMRSN SQGLSLTDSV YERLLSERII FLGSEVNDEI ANRLCAQILL LAAEDASKDI SLYINSPGGS ISAGMAIYDT MVLAPCDIA TYAMGMAASM GEFLLAAGTK GKRYALPHAR ILMHQPLGGV TGSAADIAIQ AEQFAVIKKE MFRLNAEFTG Q PIERIEAD ...String:
MSQVTDMRSN SQGLSLTDSV YERLLSERII FLGSEVNDEI ANRLCAQILL LAAEDASKDI SLYINSPGGS ISAGMAIYDT MVLAPCDIA TYAMGMAASM GEFLLAAGTK GKRYALPHAR ILMHQPLGGV TGSAADIAIQ AEQFAVIKKE MFRLNAEFTG Q PIERIEAD SDRDRWFTAA EALEYGFVDH IITRAHVNGE AQ

UniProtKB: ATP-dependent Clp protease proteolytic subunit 1

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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: 23.562754 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNSQNSQIQP QARYILPSFI EHSSFGVKES NPYNKLFEER IIFLGVQVDD ASANDIMAQL LVLESLDPDR DITMYINSPG GGFTSLMAI YDTMQYVRAD IQTVCLGQAA SAAAVLLAAG TPGKRMALPN ARVLIHQPSL SGVIQGQFSD LEIQAAEIER M RTLMETTL ...String:
MNSQNSQIQP QARYILPSFI EHSSFGVKES NPYNKLFEER IIFLGVQVDD ASANDIMAQL LVLESLDPDR DITMYINSPG GGFTSLMAI YDTMQYVRAD IQTVCLGQAA SAAAVLLAAG TPGKRMALPN ARVLIHQPSL SGVIQGQFSD LEIQAAEIER M RTLMETTL ARHTGKDAGV IRKDTDRDKI LTAEEAKDYG IIDTVLEYRK LSAQTA

UniProtKB: ATP-dependent Clp protease proteolytic subunit 2

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / 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: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 256622
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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