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- EMDB-52840: Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-52840
TitleStructure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu
Map data
Sample
  • Complex: ClpC1P1P2
    • 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: activator Bz-Leu-Leu
    • Protein or peptide: Unknown peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsprotein quality control / peptide activator / protease / ATPase / CHAPERONE
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 / ATP binding / plasma membrane / cytosol
Similarity search - Function
UVR domain / UVR domain profile. / ClpP, Ser active site / ClpA/B, conserved site 1 / Endopeptidase Clp serine active site. / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / ClpP, histidine active site / Endopeptidase Clp histidine active site. ...UVR domain / UVR domain profile. / ClpP, Ser active site / ClpA/B, conserved site 1 / Endopeptidase Clp serine active site. / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / ClpP, histidine active site / Endopeptidase Clp histidine active site. / Clp amino terminal domain, pathogenicity island component / ATP-dependent Clp protease proteolytic subunit / Clp, repeat (R) domain / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp repeat (R) domain profile. / : / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsWeinhaeupl K / Semchonok D / 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-Leu-Leu
Authors: Weinhaeupl K / Semchonok DA / Gragera M / Arranz R / Bueno Carrasco MT / Fraga H
History
DepositionFeb 17, 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

Downloads & links

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Map

FileDownload / File: emd_52840.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.525 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.075685635 - 0.33927834
Average (Standard dev.)0.00022770182 (±0.0076937866)
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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Sample components

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Entire : ClpC1P1P2

EntireName: ClpC1P1P2
Components
  • Complex: ClpC1P1P2
    • 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: activator Bz-Leu-Leu
    • Protein or peptide: Unknown peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ClpC1P1P2

SupramoleculeName: ClpC1P1P2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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 (bacteria)
Molecular weightTheoretical: 73.57568 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLVLDQFGRN LTAAAMEGKL DPVIGREKEI ERVMQVLSRR TKNNPVLIGE PGVGKTAVVE GLAQAIVHGE VPETLKDKQL YTLDLGSLV AGSRYRGDFE ERLKKVLKEI NTRGDIILFI DELHTLVGAG AAEGAIDAAS ILKPKLARGE LQTIGATTLD E YRKYIEKD ...String:
SLVLDQFGRN LTAAAMEGKL DPVIGREKEI ERVMQVLSRR TKNNPVLIGE PGVGKTAVVE GLAQAIVHGE VPETLKDKQL YTLDLGSLV AGSRYRGDFE ERLKKVLKEI NTRGDIILFI DELHTLVGAG AAEGAIDAAS ILKPKLARGE LQTIGATTLD E YRKYIEKD AALERRFQPV QVGEPTVEHT IEILKGLRDR YEAHHRVSIT DAAMVAAATL ADRYINDRFL PDKAIDLIDE AG ARMRIRR MTAPPDLREF DEKIAEARRE KESAIDAQDF EKAASLRDRE KTLVAQRAER EKQWRSGDLD VVAEVDDEQI AEV LGNWTG IPVFKLTEAE TTRLLRMEEE LHKRIIGQED AVKAVSKAIR RTRAGLKDPK RPSGSFIFAG PSGVGKTELS KALA NFLFG DDDALIQIDM GEFHDRFTAS RLFGAPPGYV GYEEGGQLTE KVRRKPFSVV LFDEIEKAHQ EIYNSLLQVL EDGRL TDGQ GRTVDFKNTV LIFTSNLGTS DISKPVGLGF SKGGGENDYE RMKQKVNDEL KKHFRPEFLN RIDDIIVFHQ LTREEI IRM VDLMISRVAG QLKSKDMALV LTDAAKALLA KRGFDPVLGA RPLRRTIQRE IEDQLSEKIL FEEVGPGQVV TVDVDNW DG EGPGEDAVFT FTGTRK

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 (bacteria)
Molecular weightTheoretical: 21.914957 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ILPSFIEHSS FGVKESNPYN KLFEERIIFL GVQVDDASAN DIMAQLLVLE SLDPDRDITM YINSPGGGFT SLMAIYDTMQ YVRADIQTV CLGQAASAAA VLLAAGTPGK RMALPNARVL IHQPSLSGVI QGQFSDLEIQ AAEIERMRTL METTLARHTG K DAGVIRKD ...String:
ILPSFIEHSS FGVKESNPYN KLFEERIIFL GVQVDDASAN DIMAQLLVLE SLDPDRDITM YINSPGGGFT SLMAIYDTMQ YVRADIQTV CLGQAASAAA VLLAAGTPGK RMALPNARVL IHQPSLSGVI QGQFSDLEIQ AAEIERMRTL METTLARHTG K DAGVIRKD TDRDKILTAE EAKDYGIIDT VLEYRKLSAQ TA

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 (bacteria)
Molecular weightTheoretical: 19.49627 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LSLTDSVYER LLSERIIFLG SEVNDEIANR LCAQILLLAA EDASKDISLY INSPGGSISA GMAIYDTMVL APCDIATYAM GMAASMGEF LLAAGTKGKR YALPHARILM HQPLGGVTGS AADIAIQAEQ FAVIKKEMFR LNAEFTGQPI ERIEADSDRD R WFTAAEAL EYGFVDHIIT R

UniProtKB: ATP-dependent Clp protease proteolytic subunit 1

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Macromolecule #4: activator Bz-Leu-Leu

MacromoleculeName: activator Bz-Leu-Leu / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 348.437 Da
SequenceString:
(S0R)L

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Macromolecule #5: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 2.230741 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / 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 #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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) / Average electron dose: 46.0 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: 3.09 Å / Resolution method: OTHER / Software - Name: cryoSPARC
Details: Average of the two focused maps that have been used to build the composite map. For the focused maps the FSC at 0.143 CUT-OFF has been used
Number images used: 71218
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9if4:
Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu

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