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- PDB-6emw: Structure of S.aureus ClpC in complex with MecA -

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Entry
Database: PDB / ID: 6emw
TitleStructure of S.aureus ClpC in complex with MecA
Components
  • (ATP-dependent Clp protease ATP-binding subunit ...) x 5
  • Adapter protein MecA
  • Class III stress response-related ATPase, AAA+ superfamily
KeywordsCHAPERONE / Chaperone / AAA+ protein / unfoldase
Function/homologyMecA, C-terminal domain superfamily / stress response to copper ion / stress response to cadmium ion / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain profile. / UVR domain / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 2 / UvrB/uvrC motif ...MecA, C-terminal domain superfamily / stress response to copper ion / stress response to cadmium ion / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain profile. / UVR domain / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 2 / UvrB/uvrC motif / Chaperonins clpA/B signature 1. / ClpA/B, conserved site 1 / Clp, N-terminal / Clp, N-terminal domain superfamily / ClpA/B family / protein metabolic process / Clp ATPase, C-terminal / Clp amino terminal domain, pathogenicity island component / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / ATPase, AAA-type, core / protein binding, bridging / ATPase family associated with various cellular activities (AAA) / AAA+ ATPase domain / pathogenesis / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Adapter protein MecA / Class III stress response-related ATPase, AAA+ superfamily / | / ATP-dependent Clp protease ATP-binding subunit ClpC / Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC
Function and homology information
Specimen sourceStaphylococcus aureus / bacteria /
MethodElectron microscopy (11 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsCarroni, M. / Mogk, A. / Bukau, B. / Franke, K.
CitationJournal: Elife / Year: 2017
Title: Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control.
Authors: Marta Carroni / Kamila B Franke / Michael Maurer / Jasmin Jäger / Ingo Hantke / Felix Gloge / Daniela Linder / Sebastian Gremer / Kürşad Turgay / Bernd Bukau / Axel Mogk
Abstract: Ring-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and ...Ring-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and substrate-specific activation. The AAA+ chaperone ClpC with the peptidase ClpP forms a bacterial protease essential to virulence and stress resistance. The adaptor MecA activates ClpC by targeting substrates and stimulating ClpC ATPase activity. We show how ClpC is repressed in its ground state by determining ClpC cryo-EM structures with and without MecA. ClpC forms large two-helical assemblies that associate via head-to-head contacts between coiled-coil middle domains (MDs). MecA converts this resting state to an active planar ring structure by binding to MD interaction sites. Loss of ClpC repression in MD mutants causes constitutive activation and severe cellular toxicity. These findings unravel an unexpected regulatory concept executed by coiled-coil MDs to tightly control AAA+ chaperone activity.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2017 / Release: Dec 27, 2017

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC
B: ATP-dependent Clp protease ATP-binding subunit ClpC
C: Class III stress response-related ATPase, AAA+ superfamily
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 ATP-binding subunit ClpC
H: ATP-dependent Clp protease ATP-binding subunit ClpC
I: Class III stress response-related ATPase, AAA+ superfamily
J: ATP-dependent Clp protease ATP-binding subunit ClpC
K: ATP-dependent Clp protease ATP-binding subunit ClpC
L: ATP-dependent Clp protease ATP-binding subunit ClpC
M: ATP-dependent Clp protease ATP-binding subunit ClpC
N: ATP-dependent Clp protease ATP-binding subunit ClpC
O: Class III stress response-related ATPase, AAA+ superfamily
P: ATP-dependent Clp protease ATP-binding subunit ClpC
Q: ATP-dependent Clp protease ATP-binding subunit ClpC
R: ATP-dependent Clp protease ATP-binding subunit ClpC
S: ATP-dependent Clp protease ATP-binding subunit ClpC
T: ATP-dependent Clp protease ATP-binding subunit ClpC
U: Class III stress response-related ATPase, AAA+ superfamily
V: ATP-dependent Clp protease ATP-binding subunit ClpC
W: ATP-dependent Clp protease ATP-binding subunit ClpC
X: ATP-dependent Clp protease ATP-binding subunit ClpC
Y: ATP-dependent Clp protease ATP-binding subunit ClpC
Z: ATP-dependent Clp protease ATP-binding subunit ClpC
a: Class III stress response-related ATPase, AAA+ superfamily
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: Adapter protein MecA
f: Adapter protein MecA
g: Adapter protein MecA
h: Adapter protein MecA
i: Adapter protein MecA
j: Adapter protein MecA
k: ATP-dependent Clp protease ATP-binding subunit ClpC
l: ATP-dependent Clp protease ATP-binding subunit ClpC
m: Class III stress response-related ATPase, AAA+ superfamily
n: ATP-dependent Clp protease ATP-binding subunit ClpC
o: ATP-dependent Clp protease ATP-binding subunit ClpC
p: ATP-dependent Clp protease ATP-binding subunit ClpC


Theoretical massNumber of molelcules
Total (without water)632,28042
Polyers632,28042
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP-dependent Clp protease ATP-binding subunit ... , 5 types, 30 molecules AGMSYkBHNTZlDJPVbnEKQWcoFLRXdp

#1: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 9325.732 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus / Gene: CA803_07045 / Production host: Escherichia coli / References: UniProt:A0A229LWI5, UniProt:Q2G0P5*PLUS
#2: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 25183.590 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus / Gene: CA803_07045 / Production host: Escherichia coli / References: UniProt:A0A229LWI5, UniProt:Q2G0P5*PLUS
#4: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 16426.250 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus / Gene: CA803_07045 / Production host: Escherichia coli / References: UniProt:A0A229LWI5, UniProt:Q2G0P5*PLUS
#5: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 19699.514 Da / Num. of mol.: 6
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1)
Strain: bovine RF122 / ET3-1 / Gene: clpC, SAB0475 / Production host: Escherichia coli / References: UniProt:Q2YSD6
#6: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 17446.889 Da / Num. of mol.: 6
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1)
Strain: bovine RF122 / ET3-1 / Gene: clpC, SAB0475 / Production host: Escherichia coli / References: UniProt:Q2YSD6

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Protein/peptide , 2 types, 12 molecules CIOUamefghij

#3: Protein/peptide
Class III stress response-related ATPase, AAA+ superfamily


Mass: 6539.123 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus / Gene: clpC, BN1321_130009 / Production host: Escherichia coli / References: UniProt:A0A0U1MEM2, UniProt:Q2G0P5*PLUS
#7: Protein/peptide
Adapter protein MecA


Mass: 10758.939 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus / Gene: mecA, ERS140147_01863 / Production host: Escherichia coli / References: UniProt:A0A077UK83, UniProt:Q2G1U5*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: ClpC in complex with MecA from S. aureus / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

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Processing

EM software
IDNameCategory
2EPUIMAGE ACQUISITION
9RELIONINITIAL EULER ASSIGNMENT
10RELIONFINAL EULER ASSIGNMENT
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 26000 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
Least-squares processHighest resolution: 11 Å

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