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- EMDB-52764: Structure of the Mycobacterium tuberculosis ClpC1P1P2 complex bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-52764
TitleStructure of the Mycobacterium tuberculosis ClpC1P1P2 complex bound to the activator Bz-LL - focused refinement ClpC1
Map data
Sample
  • Complex: ClpC1
    • Protein or peptide: ClpC1
Keywordsprotein quality control / peptide activator / protease / ATPase / CHAPERONE
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsSemchonok DA / Weinhaeupl K / Gragera M / Arranz R / Bueno Carrasco MT / Fraga H
Funding support1 items
OrganizationGrant numberCountry
Other governmentInstruct-ERIC 30641, 26164
CitationJournal: Cell Rep / Year: 2026
Title: Activation mechanism and structural assembly of the Mycobacterium tuberculosis ClpP1P2 protease and its associated ATPases.
Authors: Katharina Weinhäupl / Tatos Akopian / Dmitry A Semchonok / Olga Krandor / Rocío Arranz / M Teresa Bueno-Carrasco / Marcos Gragera / Maelenn Chevreuil / Bertrand Raynal / Samuel Zinga / ...Authors: Katharina Weinhäupl / Tatos Akopian / Dmitry A Semchonok / Olga Krandor / Rocío Arranz / M Teresa Bueno-Carrasco / Marcos Gragera / Maelenn Chevreuil / Bertrand Raynal / Samuel Zinga / Yuxin Liu / Jack Lai / WenGen Wu / William Bachovchin / Diego Gauto / Alfred Goldberg / Eric Rubin / Hugo Fraga /
Abstract: Supramolecular assemblies are fundamental to cellular biochemical processes, relying on their dynamic nature to perform essential functions. The protease ClpP1P2, in association with ATPase partners ...Supramolecular assemblies are fundamental to cellular biochemical processes, relying on their dynamic nature to perform essential functions. The protease ClpP1P2, in association with ATPase partners ClpC1 or ClpX, is critical for the survival of Mycobacterium tuberculosis (Mtb). While the ClpP1P2 complex requires activation by specific N-blocked dipeptides to exhibit proteolytic activity in vitro, the mechanism of in vivo activation remains unclear. In this study, we use cryo-electron microscopy (cryo-EM) to determine the structure of the ClpC1P1P2 complex, revealing a highly asymmetric architecture with ClpC1 bound to the ClpP1P2 protease barrel. The activator dipeptide is observed only in the ClpP2 active site, while the ClpP1 entry pore remains closed. Molecular crowding agents promote the formation of larger ClpXP1P2 and ClpC1P1P2 complexes, enhancing structural stability and enzymatic activity. These findings suggest that molecular crowding stabilizes these complexes and promotes their activation, providing new insights into ClpC1P1P2 structural dynamics and function.
History
DepositionFeb 7, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52764.png

Downloads & links

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Map

FileDownload / File: emd_52764.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.525 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.0388474 - 0.09713463
Average (Standard dev.)-0.00010823683 (±0.002712989)
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_52764_msk_1.map
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Additional map: #1

Fileemd_52764_additional_1.map
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Half map: #1

Fileemd_52764_half_map_1.map
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Half map: #2

Fileemd_52764_half_map_2.map
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Sample components

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Entire : ClpC1

EntireName: ClpC1
Components
  • Complex: ClpC1
    • Protein or peptide: ClpC1

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Supramolecule #1: ClpC1

SupramoleculeName: ClpC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: ClpC1

MacromoleculeName: ClpC1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFERFTDRAR RVVVLAQEEA RMLNHNYIGT EHILLGLIHE GEGVAAKSLE SLGISLEGVR SQVEEIIGQ GQQAPSGHIP FTPRAKKVLE LSLREALQLG HNYIGTEHIL LGLIREGEGV A AQVLVKLG AELTRVRQQV IQLLSGYQGK EAAEAGTGGR GGESGSPSTS ...String:
MFERFTDRAR RVVVLAQEEA RMLNHNYIGT EHILLGLIHE GEGVAAKSLE SLGISLEGVR SQVEEIIGQ GQQAPSGHIP FTPRAKKVLE LSLREALQLG HNYIGTEHIL LGLIREGEGV A AQVLVKLG AELTRVRQQV IQLLSGYQGK EAAEAGTGGR GGESGSPSTS LVLDQFGRNL TA AAMEGKL DPVIGREKEI ERVMQVLSRR TKNNPVLIGE PGVGKTAVVE GLAQAIVHGE VPE TLKDKQ LYTLDLGSLV AGSRYRGDFE ERLKKVLKEI NTRGDIILFI DELHTLVGAG AAEG AIDAA SILKPKLARG ELQTIGATTL DEYRKYIEKD AALERRFQPV QVGEPTVEHT IEILK GLRD RYEAHHRVSI TDAAMVAAAT LADRYINDRF LPDKAIDLID EAGARMRIRR MTAPPD LRE FDEKIAEARR EKESAIDAQD AEKAASLRDR EKTLVAQRAE REKQWRSGDL DVVAEVD DE QIAEVLGNWT GIPVFKLTEA ETTRLLRMEE ELHKRIIGQE DAVKAVSKAI RRTRAGLK D PKRPSGSFIF AGPSGVGKTE LSKALANFLF GDDDALIQID MGEFHDRFTA SRLFGAPPG YVGYEEGGQL TEKVRRKPFS VVLFDEIEKA HQEIYNSLLQ VLEDGRLTDG QGRTVDFKNT VLIFTSNLG TSDISKPVGL GFSKGGGEND YERMKQKVND ELKKHFRPEF LNRIDDIIVF H QLTREEII RMVDLMISRV AGQLKSKDMA LVLTDAAKAL LAKRGFDPVL GARPLRRTIQ RE IEDQLSE KILFEEVGPG QVVTVDVDNW DGEGPGEDAV FTFTGTRKPP AEPDLAKAGA HSA GGPEPA AR

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 71279
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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