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

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Basic information

Entry
Database: PDB / ID: 6emw
TitleStructure of S.aureus ClpC in complex with MecA
Components
  • (ATP-dependent Clp protease ATP-binding ...) x 5
  • Adapter protein MecA
  • Class III stress response-related ATPase, AAA+ superfamily
KeywordsCHAPERONE / AAA+ protein / unfoldase
Function / homology
Function and homology information


stress response to cadmium ion / stress response to copper ion / protein-macromolecule adaptor activity / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding
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. / ClpA/ClpB, AAA lid domain ...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. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / 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 / 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
Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC / : / ATP-dependent Clp protease ATP-binding subunit / ATP-dependent Clp protease ATP-binding subunit ClpC / Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11 Å
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 substrate- ...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.
History
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Revision 1.2Sep 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: database_PDB_caveat / entity ...database_PDB_caveat / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

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Structure visualization

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit
B: ATP-dependent Clp protease ATP-binding subunit
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
H: ATP-dependent Clp protease ATP-binding subunit
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
N: ATP-dependent Clp protease ATP-binding subunit
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
T: ATP-dependent Clp protease ATP-binding subunit
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
Z: ATP-dependent Clp protease ATP-binding subunit
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
l: ATP-dependent Clp protease ATP-binding subunit
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
Polymers632,28042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

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


Mass: 9325.732 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: E1951_02375, E1E62_02425, FF957_02715 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V1GG18, UniProt: Q2G0P5*PLUS
#2: Protein
ATP-dependent Clp protease ATP-binding subunit


Mass: 25183.590 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: E1949_02445, E1952_02450, E1E63_02625 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P9AXU9, UniProt: Q2G0P5*PLUS
#4: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC / Clp protease ATP binding subunit / Clp protease ClpX / Endopeptidase Clp ATP-binding subunit C / Hemolysin B


Mass: 16426.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: clpC, clpC_1, BTN44_10070, C7P97_07760, CSC83_01585, CSC87_01340, EP54_12860, EQ90_07030, ER624_03540, ERS072840_00763, HMPREF3211_01370, M1K003_1986, NCTC10654_00620, NCTC13131_01061, RK64_ ...Gene: clpC, clpC_1, BTN44_10070, C7P97_07760, CSC83_01585, CSC87_01340, EP54_12860, EQ90_07030, ER624_03540, ERS072840_00763, HMPREF3211_01370, M1K003_1986, NCTC10654_00620, NCTC13131_01061, RK64_03235, SAMEA1708674_02933
Production host: Escherichia coli (E. coli) / References: UniProt: W8U1E4, UniProt: Q2G0P5*PLUS
#5: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC


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


Mass: 17446.889 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: clpC, SAB0475 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YSD6

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Protein , 2 types, 12 molecules CIOUamefghij

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


Mass: 6539.123 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpC, BN1321_130009 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1MEM2, UniProt: Q2G0P5*PLUS
#7: Protein
Adapter protein MecA /


Mass: 10758.939 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecA, ERS140147_01863 / Production host: Escherichia coli (E. 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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ClpC in complex with MecA from S. aureusList of electric distribution utilities in the Philippines
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / 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 (asymmetric)
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 11 Å

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