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- EMDB-3897: Structure of S.aureus ClpC in complex with MecA -

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Basic information

Entry
Database: EMDB / ID: 3897
TitleStructure of S.aureus ClpC in complex with MecA
Map dataLow-resolution map of S.aureus ClpC in complex with MecA
SampleClpC in complex with MecA from S. aureus
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
SourceStaphylococcus aureus / bacteria /
Methodsingle particle reconstruction, at 11 Å resolution
AuthorsCarroni M / Mogk A
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 ReportPDB-ID: 6emw

SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6emw
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3897.map.gz (map file in CCP4 format, 70305 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
1.36 Å/pix.
= 353.6 Å
260 pix
1.36 Å/pix.
= 353.6 Å
260 pix
1.36 Å/pix.
= 353.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour Level:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.022201095 - 0.06874993
Average (Standard dev.)0.00058354076 (0.0036839915)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions260260260
Origin000
Limit259259259
Spacing260260260
CellA=B=C: 353.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z353.600353.600353.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0220.0690.001

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Supplemental data

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Mask #1

Fileemd_3897_msk_1.map ( map file in CCP4 format, 70305 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsLow-resolution map of S.aureus ClpC in complex with MecA, mask
Space group number1

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Mask #1~

Fileemd_3897_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire ClpC in complex with MecA from S. aureus

EntireName: ClpC in complex with MecA from S. aureus / Number of components: 8

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Component #1: protein, ClpC in complex with MecA from S. aureus

ProteinName: ClpC in complex with MecA from S. aureus / Recombinant expression: No
SourceSpecies: Staphylococcus aureus / bacteria /
Source (engineered)Expression System: Escherichia coli / bacteria / /

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Component #2: protein, ATP-dependent Clp protease ATP-binding subunit ClpC

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Recombinant expression: No
MassTheoretical: 9.325732 kDa
Source (engineered)Expression System: Staphylococcus aureus / bacteria /

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Component #3: protein, ATP-dependent Clp protease ATP-binding subunit ClpC

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Recombinant expression: No
MassTheoretical: 25.18359 kDa
Source (engineered)Expression System: Staphylococcus aureus / bacteria /

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Component #4: protein, Class III stress response-related ATPase, AAA+ superfamily

ProteinName: Class III stress response-related ATPase, AAA+ superfamily
Recombinant expression: No
MassTheoretical: 6.539123 kDa
Source (engineered)Expression System: Staphylococcus aureus / bacteria /

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Component #5: protein, ATP-dependent Clp protease ATP-binding subunit ClpC

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Recombinant expression: No
MassTheoretical: 16.42625 kDa
Source (engineered)Expression System: Staphylococcus aureus / bacteria /

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Component #6: protein, ATP-dependent Clp protease ATP-binding subunit ClpC

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Recombinant expression: No
MassTheoretical: 19.699514 kDa
Source (engineered)Expression System: Staphylococcus aureus (strain bovine rf122 / et3-1) / bacteria /
Strain: bovine RF122 / ET3-1

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Component #7: protein, ATP-dependent Clp protease ATP-binding subunit ClpC

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Recombinant expression: No
MassTheoretical: 17.446889 kDa
Source (engineered)Expression System: Staphylococcus aureus (strain bovine rf122 / et3-1) / bacteria /
Strain: bovine RF122 / ET3-1

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Component #8: protein, Adapter protein MecA

ProteinName: Adapter protein MecA / Recombinant expression: No
MassTheoretical: 10.758939 kDa
Source (engineered)Expression System: Staphylococcus aureus / bacteria /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.25 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 26000
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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