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- EMDB-3894: S.aureus ClpC resting state, C2 symmetrised -

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Basic information

Entry
Database: EMDB / ID: 3894
TitleS.aureus ClpC resting state, C2 symmetrised
Map dataResting state of ClpC from S. aureus. C2 symmetry applied.
SampleResting-state oligomeric complex of S. aureus ClpC
  • ATP-dependent Clp protease ATP-binding subunit ClpC
Function / homologyClp ATPase, C-terminal / UVR domain profile. / Chaperonins clpA/B signature 1. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Clp amino terminal domain, pathogenicity island component / ATPase family associated with various cellular activities (AAA) / Clp, N-terminal domain superfamily / ClpA/B, conserved site 2 / P-loop containing nucleoside triphosphate hydrolase ...Clp ATPase, C-terminal / UVR domain profile. / Chaperonins clpA/B signature 1. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Clp amino terminal domain, pathogenicity island component / ATPase family associated with various cellular activities (AAA) / Clp, N-terminal domain superfamily / ClpA/B, conserved site 2 / P-loop containing nucleoside triphosphate hydrolase / ClpA/B, conserved site 1 / Clp, N-terminal / ATPase, AAA-type, core / AAA+ ATPase domain / UVR domain / ClpA/B family / Chaperonins clpA/B signature 2. / stress response to cadmium ion / stress response to copper ion / protein metabolic process / peptidase activity / pathogenesis / ATP binding / ATP-dependent Clp protease ATP-binding subunit ClpC / ATP-dependent Clp protease ATP-binding subunit ClpC
Function and homology information
SourceStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / 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
Validation ReportPDB-ID: 6em8

SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6em8
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

Fileemd_3894.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.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.15715489 - 0.25433508
Average (Standard dev.)0.0010562415 (0.010013308)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 402.0 Å
α=β=γ: 90.0 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-0.1570.2540.001

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Supplemental data

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Mask #1

Fileemd_3894_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

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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)
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 91.170352 kDa
SourceSpecies: Staphylococcus aureus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 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: C2 (2 fold cyclic) / Number of projections: 40000
3D reconstructionSoftware: RELION / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL / Details: Phyre2 base on the crystal structure PDB: 3pxi
Output model

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