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- PDB-9rai: Structure of the S.aureus MecA/ClpC/ClpP degradation system -

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Basic information

Entry
Database: PDB / ID: 9rai
TitleStructure of the S.aureus MecA/ClpC/ClpP degradation system
Components
  • (ATP-dependent Clp protease ...) x 2
  • Adapter protein MecA
  • unknown substrate
KeywordsCHAPERONE / protein-quality control / AAA+ unfoldases / peptidases / adaptor proteins
Function / homology
Function and homology information


stress response to cadmium ion / stress response to copper ion / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / protein-macromolecule adaptor activity / serine-type endopeptidase activity / ATP hydrolysis activity ...stress response to cadmium ion / stress response to copper ion / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / protein-macromolecule adaptor activity / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpP, Ser active site ...MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpP, Ser active site / ClpA/ClpB, AAA lid domain / AAA lid domain / Endopeptidase Clp serine active site. / Clp amino terminal domain, pathogenicity island component / ClpP, histidine active site / Endopeptidase Clp histidine active site. / : / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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 / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Adapter protein MecA / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsAzinas, S. / Wallden, K. / Katikaridis, P. / Schahl, A. / Mogk, A. / Carroni, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP
Authors: Azinas, S. / Wallden, K. / Katikaridis, P. / Schahl, A. / Mogk, A. / Carroni, M.
History
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 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

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Assembly

Deposited unit
A: Adapter protein MecA
B: Adapter protein MecA
C: Adapter protein MecA
D: Adapter protein MecA
E: Adapter protein MecA
F: Adapter protein MecA
S: unknown substrate
a: ATP-dependent Clp protease ATP-binding subunit ClpC
b: ATP-dependent Clp protease ATP-binding subunit ClpC
c: ATP-dependent Clp protease ATP-binding subunit ClpC
d: ATP-dependent Clp protease ATP-binding subunit ClpC
e: ATP-dependent Clp protease ATP-binding subunit ClpC
f: ATP-dependent Clp protease ATP-binding subunit ClpC
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,025,22744
Polymers1,020,20827
Non-polymers5,01817
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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ATP-dependent Clp protease ... , 2 types, 20 molecules abcdefGHIJKLMNOPQRTU

#3: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 91170.352 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpC, SAOUHSC_00505 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G0P5
#4: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 21536.531 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpP, SAOUHSC_00790 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G036, endopeptidase Clp

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFS

#1: Protein
Adapter protein MecA


Mass: 28354.170 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecA, SAUSA300_0899 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FI79
#2: Protein/peptide unknown substrate


Mass: 1549.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 17 molecules

#5: 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
#6: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: Complex of 6 copies of S.aureus ClpC (without the N terminal and M-domain) plus 14 copies of S.aureus ClpP
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.800 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus (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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topaz0.25particle selection
2EPU3.7image acquisition
4cryoSPARC4.3CTF correction
9PHENIX1.21_5207model refinement
10Servalcat0.2.137model refinement
12cryoSPARC4.3final Euler assignment
14cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2851121
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82854 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.89 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003461791
ELECTRON MICROSCOPYf_angle_d0.650983443
ELECTRON MICROSCOPYf_chiral_restr0.04339663
ELECTRON MICROSCOPYf_plane_restr0.004410823
ELECTRON MICROSCOPYf_dihedral_angle_d7.15698451

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