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- PDB-9if4: Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bou... -

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Basic information

Entry
Database: PDB / ID: 9if4
TitleStructure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu
Components
  • (ATP-dependent Clp protease proteolytic subunit ...) x 2
  • ATP-dependent Clp protease ATP-binding subunit ClpC1
  • Unknown peptide
  • activator Bz-Leu-Leu
KeywordsCHAPERONE / protein quality control / peptide activator / protease / ATPase
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsWeinhaeupl, K. / Semchonok, D. / Gragera, M. / Arranz, R. / Bueno Carrasco, M.T. / Fraga, H.
Funding support1items
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, D.A. / Gragera, M. / Arranz, R. / Bueno Carrasco, M.T. / Fraga, H.
History
DepositionFeb 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC1
B: ATP-dependent Clp protease ATP-binding subunit ClpC1
C: ATP-dependent Clp protease ATP-binding subunit ClpC1
D: ATP-dependent Clp protease ATP-binding subunit ClpC1
E: ATP-dependent Clp protease ATP-binding subunit ClpC1
F: ATP-dependent Clp protease ATP-binding subunit ClpC1
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 2
I: ATP-dependent Clp protease proteolytic subunit 2
J: ATP-dependent Clp protease proteolytic subunit 2
L: ATP-dependent Clp protease proteolytic subunit 2
M: ATP-dependent Clp protease proteolytic subunit 2
N: ATP-dependent Clp protease proteolytic subunit 1
O: ATP-dependent Clp protease proteolytic subunit 1
P: ATP-dependent Clp protease proteolytic subunit 1
Q: ATP-dependent Clp protease proteolytic subunit 1
R: ATP-dependent Clp protease proteolytic subunit 1
S: ATP-dependent Clp protease proteolytic subunit 1
T: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 2
U: activator Bz-Leu-Leu
V: activator Bz-Leu-Leu
W: activator Bz-Leu-Leu
Y: activator Bz-Leu-Leu
Z: activator Bz-Leu-Leu
a: activator Bz-Leu-Leu
b: activator Bz-Leu-Leu
X: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)741,76940
Polymers736,00228
Non-polymers5,76612
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC1


Mass: 73575.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9

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ATP-dependent Clp protease proteolytic subunit ... , 2 types, 14 molecules GHIJLMKNOPQRST

#2: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 21914.957 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpP2, Rv2460c, MTV008.16c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC3, endopeptidase Clp
#3: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 19496.270 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpP1, clpP, Rv2461c, MTV008.17c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC5, endopeptidase Clp

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Protein/peptide , 2 types, 8 molecules UVWYZabX

#4: Protein/peptide
activator Bz-Leu-Leu


Mass: 348.437 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Protein/peptide Unknown peptide


Mass: 2230.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 12 molecules

#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ClpC1P1P2 / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingElectron dose: 46 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6.0particle selection
4cryoSPARC4.6.0CTF correctionPatch CTF
9PHENIX1.21.1_5286model refinement
10cryoSPARC4.6.0initial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1372648
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.09 Å / Resolution method: OTHER / Num. of particles: 71218 / Algorithm: FOURIER SPACE
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
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005945795
ELECTRON MICROSCOPYf_angle_d0.515661809
ELECTRON MICROSCOPYf_chiral_restr0.0417128
ELECTRON MICROSCOPYf_plane_restr0.00557958
ELECTRON MICROSCOPYf_dihedral_angle_d6.82986395

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