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

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Basic information

Entry
Database: EMDB / ID: EMD-3894
TitleS.aureus ClpC resting state, C2 symmetrised
Map dataResting state of ClpC from S. aureus. C2 symmetry applied.
Sample
  • Complex: Resting-state oligomeric complex of S. aureus ClpC
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
Function / homology
Function and homology information


stress response to cadmium ion / stress response to copper ion / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding
Similarity search - Function
UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. ...UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent Clp protease ATP-binding subunit ClpC / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
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 substrate- ...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.
History
DepositionOct 1, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseDec 27, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3894.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationResting state of ClpC from S. aureus. C2 symmetry applied.
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.15715489 - 0.25433508
Average (Standard dev.)0.0010562415 (±0.010013308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 402.0 Å
α=β=γ: 90.0 °

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
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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Half map: Half map 1. Resting state of ClpC from...

Fileemd_3894_half_map_1.map
AnnotationHalf map 1. Resting state of ClpC from S. aureus. C2 symmetry applied.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 2. Resting state of ClpC from...

Fileemd_3894_half_map_2.map
AnnotationHalf map 2. Resting state of ClpC from S. aureus. C2 symmetry applied.
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
Components
  • Complex: Resting-state oligomeric complex of S. aureus ClpC
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC

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Supramolecule #1: Resting-state oligomeric complex of S. aureus ClpC

SupramoleculeName: Resting-state oligomeric complex of S. aureus ClpC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 900 KDa

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Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpC

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 91.170352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLFGRLTERA QRVLAHAQEE AIRLNHSNIG TEHLLLGLMK EPEGIAAKVL ESFNITEDKV IEEVEKLIGH GQDHVGTLHY TPRAKKVIE LSMDEARKLH HNFVGTEHIL LGLIRENEGV AARVFANLDL NITKARAQVV KALGNPEMSN KNAQASKSNN T PTLDSLAR ...String:
MLFGRLTERA QRVLAHAQEE AIRLNHSNIG TEHLLLGLMK EPEGIAAKVL ESFNITEDKV IEEVEKLIGH GQDHVGTLHY TPRAKKVIE LSMDEARKLH HNFVGTEHIL LGLIRENEGV AARVFANLDL NITKARAQVV KALGNPEMSN KNAQASKSNN T PTLDSLAR DLTVIAKDGT LDPVIGRDKE ITRVIEVLSR RTKNNPVLIG EPGVGKTAIA EGLAQAIVNN EVPETLKDKR VM SLDMGTV VAGTKYRGEF EERLKKVMEE IQQAGNVILF IDELHTLVGA GGAEGAIDAS NILKPALARG ELQCIGATTL DEY RKNIEK DAALERRFQP VQVDEPSVVD TVAILKGLRD RYEAHHRINI SDEAIEAAVK LSNRYVSDRF LPDKAIDLID EASS KVRLK SHTTPNNLKE IEQEIEKVKN EKDAAVHAQE FENAANLRDK QTKLEKQYEE AKNEWKNAQN GMSTSLSEED IAEVI AGWT GIPLTKINET ESEKLLSLED TLHERVIGQK DAVNSISKAV RRARAGLKDP KRPIGSFIFL GPTGVGKTEL ARALAE SMF GDDDAMIRVD MSEFMEKHAV SRLVGAPPGY VGHDDGGQLT EKVRRKPYSV ILFDEIEKAH PDVFNILLQV LDDGHLT DT KGRTVDFRNT IIIMTSNVGA QELQDQRFAG FGGSSDGQDY ETIRKTMLKE LKNSFRPEFL NRVDDIIVFH KLTKEELK E IVTMMVNKLT NRLSEQNINI IVTDKAKDKI AEEGYDPEYG ARPLIRAIQK TIEDNLSELI LDGNQIEGKK VTVDHDGKE FKYDIAEQTS ETKTPSQA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV
Detailsconcentration used was 6uM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: Stochastic Gradient Descent
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.3)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.6) / Number images used: 40000
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsPhyre2 base on the crystal structure PDB: 3pxi
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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