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- EMDB-3895: S.aureus ClpC resting state, asymmetric map -

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Basic information

Entry
Database: EMDB / ID: 3895
TitleS.aureus ClpC resting state, asymmetric map
Map data
SampleResting-state oligomeric complex of S. aureus ClpC
  • ATP-dependent Clp protease ATP-binding subunit ClpC
Function/homologyUVR domain profile. / UVR domain / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / UvrB/uvrC motif / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / Clp, N-terminal / Clp, N-terminal domain superfamily / ClpA/B family ...UVR domain profile. / UVR domain / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / UvrB/uvrC motif / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 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 / ATPase family associated with various cellular activities (AAA) / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ATP-dependent Clp protease ATP-binding subunit ClpC
Function and homology information
SourceStaphylococcus aureus / / bacteria
MethodCryo EM / single particle reconstruction / 8.4 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: 6em9

SummaryFull reportAbout validation report
DateDeposition: Oct 1, 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: 1.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1.1
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6em9
  • Surface level: 1.1
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3895.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.34 Å/pix.
= 402. Å
300 pix
1.34 Å/pix.
= 402. Å
300 pix
1.34 Å/pix.
= 402. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:1.1 (by author), 1.1 (movie #1):
Minimum - Maximum-1.4772109 - 2.9576414
Average (Standard dev.)0.015657905 (0.16767722)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 402 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z402.000402.000402.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.4772.9580.016

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Supplemental data

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Mask #1

Fileemd_3895_msk_1.map ( map file in CCP4 format, 108001 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3895_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Resting-state oligomeric complex of S. aureus ClpC

EntireName: Resting-state oligomeric complex of S. aureus ClpC / Number of components: 2
MassExperimental: 900 kDa

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Component #1: protein, Resting-state oligomeric complex of S. aureus ClpC

ProteinName: Resting-state oligomeric complex of S. aureus ClpC / Recombinant expression: No
MassExperimental: 900 kDa
SourceSpecies: Staphylococcus aureus / / bacteria / Strain: bovine RF122 / ET3-1
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: 91.200375 kDa
Source (engineered)Expression System: Staphylococcus aureus (strain bovine rf122 / et3-1) / / bacteria
Strain: bovine RF122 / ET3-1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 297 K / Humidity: 100 %

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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: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 40000
3D reconstructionSoftware: RELION / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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