[English] 日本語
Yorodumi
- EMDB-52766: Structure of the Mycobacterium tuberculosis ClpC1P1P2 complex bou... -

+
Open data


ID or keywords:

Loading...

-
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: 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

-
Structure visualization

Supplemental images

emd_52766.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_52766_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_52766_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52766_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52766_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
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)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more