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- EMDB-52766: Structure of the Mycobacterium tuberculosis ClpC1P1P2 complex bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-52766
TitleStructure of the Mycobacterium tuberculosis ClpC1P1P2 complex bound to the activator Bz-LL - focused map ClpP1P2
Map data
Sample
  • Complex: ClpP1P2 bound to Bz-LL
    • Protein or peptide: ClpP1
    • Protein or peptide: ClpP2
Keywordsprotein quality control / peptide activator / protease / ATPase / CHAPERONE
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSemchonok D / Weinhaeupl K / Gragera M / Arranz R / Bueno Carrasco MT / Fraga H
Funding support1 items
OrganizationGrant numberCountry
Other governmentInstruct-ERIC 30641, 26164
CitationJournal: To Be Published
Title: Structure of the Mycobacterium tuberculosis ClpC1P1P2 complex bound to the activator Bz-LL - focused map ClpP1P2
Authors: Semchonok DA / Weinhaeupl K / Gragera M / Arranz R / Bueno Carrasco MT / Fraga H
History
DepositionFeb 7, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52766.png

Downloads & links

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Map

FileDownload / File: emd_52766.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 600 pix.
= 315. Å		0.53 Å/pix.
x 600 pix.
= 315. Å		0.53 Å/pix.
x 600 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.525 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0239
Minimum - Maximum-0.082206585 - 0.19616503
Average (Standard dev.)-0.00024012566 (±0.0063301693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52766_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_52766_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_52766_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52766_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : ClpP1P2 bound to Bz-LL

EntireName: ClpP1P2 bound to Bz-LL
Components
  • Complex: ClpP1P2 bound to Bz-LL
    • Protein or peptide: ClpP1
    • Protein or peptide: ClpP2

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Supramolecule #1: ClpP1P2 bound to Bz-LL

SupramoleculeName: ClpP1P2 bound to Bz-LL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: ClpP1

MacromoleculeName: ClpP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQVTDMRSN SQGLSLTDSV YERLLSERII FLGSEVNDEI ANRLCAQILL LAAEDASKDI SLYINSPGGS ISAGMAIYDT MVLAPCDIAT YAMGMAASMG EFLLAAGTKG KRYALPHARI LMHQPLGGVT GSAADIAIQA EQFAVIKKEM FRLNAEFTGQ PIERIEADSD ...String:
MSQVTDMRSN SQGLSLTDSV YERLLSERII FLGSEVNDEI ANRLCAQILL LAAEDASKDI SLYINSPGGS ISAGMAIYDT MVLAPCDIAT YAMGMAASMG EFLLAAGTKG KRYALPHARI LMHQPLGGVT GSAADIAIQA EQFAVIKKEM FRLNAEFTGQ PIERIEADSD RDRWFTAAEA LEYGFVDHII TRAHVNGEAQ

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Macromolecule #2: ClpP2

MacromoleculeName: ClpP2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSQNSQIQP QARYILPSFI EHSSFGVKES NPYNKLFEER IIFLGVQVDD ASANDIMAQL LVLESLDPDR DITMYINSPG GGFTSLMAIY DTMQYVRADI QTVCLGQAAS AAAVLLAAGT PGKRMALPNA RVLIHQPSLS GVIQGQFSDL EIQAAEIERM RTLMETTLAR ...String:
MNSQNSQIQP QARYILPSFI EHSSFGVKES NPYNKLFEER IIFLGVQVDD ASANDIMAQL LVLESLDPDR DITMYINSPG GGFTSLMAIY DTMQYVRADI QTVCLGQAAS AAAVLLAAGT PGKRMALPNA RVLIHQPSLS GVIQGQFSDL EIQAAEIERM RTLMETTLAR HTGKDAGVIR KDTDRDKILT AEEAKDYGII DTVLEYRKLS AQTA

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 77.0 K / Max: 77.0 K
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 10943 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1372648
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 10 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 71218
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 15000 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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