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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
  • (ATP-dependent Clp protease ATP-binding subunit ...) x 5
  • Class III stress response-related ATPase, AAA+ superfamily
  • Adapter protein MecA
Function / homologyClp, N-terminal domain superfamily / UVR domain profile. / Chaperonins clpA/B signature 1. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Negative regulator of genetic competence (MecA) / Clp amino terminal domain, pathogenicity island component / UvrB/uvrC motif / ATPase family associated with various cellular activities (AAA) / MecA, C-terminal domain superfamily ...Clp, N-terminal domain superfamily / UVR domain profile. / Chaperonins clpA/B signature 1. / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Negative regulator of genetic competence (MecA) / Clp amino terminal domain, pathogenicity island component / UvrB/uvrC motif / ATPase family associated with various cellular activities (AAA) / MecA, C-terminal domain superfamily / ClpA/B, conserved site 2 / P-loop containing nucleoside triphosphate hydrolase / Clp ATPase, C-terminal / ClpA/B, conserved site 1 / Negative regulator of genetic competence, MecA / 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 / protein binding, bridging / pathogenesis / ATP binding / Adapter protein MecA / Class III stress response-related ATPase, AAA+ superfamily / un:a0a229lwi5: / 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) / Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Methodsingle particle reconstruction / cryo EM / 11 Å resolution
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
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: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

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
Origin0.00.00.0
Limit259.0259.0259.0
Spacing260260260
CellA=B=C: 353.6 Å
α=β=γ: 90.0 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
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 (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: 6 / Recombinant expression: No
MassTheoretical: 9.325732 kDa
SourceSpecies: Staphylococcus aureus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 25.18359 kDa
SourceSpecies: Staphylococcus aureus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: Class III stress response-related ATPase, AAA+ superfamily
Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.539123 kDa
SourceSpecies: Staphylococcus aureus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 16.42625 kDa
SourceSpecies: Staphylococcus aureus (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 19.699514 kDa
SourceSpecies: Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1
Source (engineered)Expression System: Escherichia coli (E. coli)

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

ProteinName: ATP-dependent Clp protease ATP-binding subunit ClpC / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 17.446889 kDa
SourceSpecies: Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Adapter protein MecA

ProteinName: Adapter protein MecA / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 10.758939 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
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: 1000.0 - 3000.0 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (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 estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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