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- PDB-6em8: S.aureus ClpC resting state, C2 symmetrised -

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Basic information

Entry
Database: PDB / ID: 6em8
TitleS.aureus ClpC resting state, C2 symmetrised
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC
KeywordsCHAPERONE / ClpC / AAA+ protease / oligomeric complex
Function / homologyAAA lid domain / Clp ATPase, C-terminal / UVR domain profile. / Chaperonins clpA/B signature 2. / 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 ...AAA lid domain / Clp ATPase, C-terminal / UVR domain profile. / Chaperonins clpA/B signature 2. / 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 / 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
Specimen sourceStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn

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Structure visualization

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC
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: 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 ClpC
I: ATP-dependent Clp protease ATP-binding subunit ClpC
H: ATP-dependent Clp protease ATP-binding subunit ClpC
L: ATP-dependent Clp protease ATP-binding subunit ClpC


Theoretical massNumber of molelcules
Total (without water)911,70410
Polyers911,70410
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC / Endopeptidase Clp ATP-binding subunit C / Hemolysin B


Mass: 91170.352 Da / Num. of mol.: 10 / Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: clpC, BER48_000499, CEJ93_12415, ERS072738_00457, ERS072840_00763, ERS073583_01020, ERS074020_00452, HMPREF3211_01370
Production host: Escherichia coli (E. coli) / References: UniProt: W8U1E4, UniProt: Q2G0P5*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Resting-state oligomeric complex of S. aureus ClpC / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.9 MDa / Experimental value: YES
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenDetails: concentration used was 6uM / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7iMODFITmodel fitting
10RELION2.3final Euler assignment
12RELION2.63D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 40000 / Symmetry type: POINT
Atomic model buildingDetails: Phyre2 base on the crystal structure PDB: 3pxi / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Least-squares processHighest resolution: 8.4 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01851651
ELECTRON MICROSCOPYf_angle_d1.62769409
ELECTRON MICROSCOPYf_dihedral_angle_d8.32532159
ELECTRON MICROSCOPYf_chiral_restr0.0768046
ELECTRON MICROSCOPYf_plane_restr0.0109041

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