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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: EMD-3897
TitleStructure of S.aureus ClpC in complex with MecA
Map dataLow-resolution map of S.aureus ClpC in complex with MecA
Sample
  • Complex: ClpC in complex with MecA from S. aureus
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit
    • Protein or peptide: Class III stress response-related ATPase, AAA+ superfamily
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: Adapter protein MecA
KeywordsChaperone / AAA+ protein / unfoldase
Function / homology
Function and homology information


stress response to cadmium ion / stress response to copper ion / peptidase activity / cellular response to heat / protein-macromolecule adaptor activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / 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 ...MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / 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 / Clp repeat (R) domain profile. / 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
Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC / : / ATP-dependent Clp protease ATP-binding subunit / ATP-dependent Clp protease ATP-binding subunit ClpC / Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria) / Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 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 3, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseDec 27, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • 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

emd_3897.png

Downloads & links

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Map

FileDownload / File: emd_3897.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow-resolution map of S.aureus ClpC in complex with MecA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 260 pix.
= 353.6 Å		1.36 Å/pix.
x 260 pix.
= 353.6 Å		1.36 Å/pix.
x 260 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.022201095 - 0.06874993
Average (Standard dev.)0.00058354076 (±0.0036839915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 353.6 Å
α=β=γ: 90.0 °

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
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

Histogram

Histogram (log scale)

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Half map: Low-resolution map of S.aureus ClpC in complex with MecA, half mapA

Fileemd_3897_half_map_1.map
AnnotationLow-resolution map of S.aureus ClpC in complex with MecA, half mapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Low-resolution map of S.aureus ClpC in complex with MecA, half mapB

Fileemd_3897_half_map_2.map
AnnotationLow-resolution map of S.aureus ClpC in complex with MecA, half mapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Components
  • Complex: ClpC in complex with MecA from S. aureus
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit
    • Protein or peptide: Class III stress response-related ATPase, AAA+ superfamily
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: Adapter protein MecA

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Supramolecule #1: ClpC in complex with MecA from S. aureus

SupramoleculeName: ClpC in complex with MecA from S. aureus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

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

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 9.325732 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KLTKEELKEI VTMMVNKLTN RLSEQNINII VTDKAKDKIA EEGYDPEYGA RPLIRAIQKT IEDNLSELIL DGNQIEGKKV TV

UniProtKB: ATP-dependent Clp protease ATP-binding subunit

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Macromolecule #2: ATP-dependent Clp protease ATP-binding subunit

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 25.18359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LTKINETESE KLLSLEDTLH ERVIGQKDAV NSISKAVRRA RAGLKDPKRP IGSFIFLGPT GVGKTELARA LAESMFGDDD AMIRVDMSE FMEKHAVSRL VGAPPGYVGH DDGGQLTEKV RRKPYSVILF DEIEKAHPDV FNILLQVLDD GHLTDTKGRT V DFRNTIII ...String:
LTKINETESE KLLSLEDTLH ERVIGQKDAV NSISKAVRRA RAGLKDPKRP IGSFIFLGPT GVGKTELARA LAESMFGDDD AMIRVDMSE FMEKHAVSRL VGAPPGYVGH DDGGQLTEKV RRKPYSVILF DEIEKAHPDV FNILLQVLDD GHLTDTKGRT V DFRNTIII MTSNVGAQEL QDQRFAGFGG SSDGQDYETI RKTMLKELKN SFRPEFLNRV DDIIVFH

UniProtKB: UNIPROTKB: A0A4P9AXU9

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Macromolecule #3: Class III stress response-related ATPase, AAA+ superfamily

MacromoleculeName: Class III stress response-related ATPase, AAA+ superfamily
type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 6.539123 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NNLKEIEQEI EKVKNEKDAA VHAQEFENAA NLRDKQTKLE KQYEEAKNEW KNAQN

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpC

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Macromolecule #4: ATP-dependent Clp protease ATP-binding subunit ClpC

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 16.42625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SVVDTVAILK GLRDRYEAHH RINISDEAIE AAVKLSNRYV SDRFLPDKAI DLIDEASSKV RLKSHTTPNN LKEIEQEIEK VKNEKDAAV HAQEFENAAN LRDKQTKLEK QYEEAKNEWK NAQNGMSTSL SEEDIAEVIA GWTGIP

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpC

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Macromolecule #5: ATP-dependent Clp protease ATP-binding subunit ClpC

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1
Molecular weightTheoretical: 19.699514 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TLDSLARDLT VIAKDGTLDP VIGRDKEITR VIEVLSRRTK NNPVLIGEPG VGKTAIAEGL AQAIVNNEVP ETLKDKRVMS LDMGTVVAG TKYRGEFEER LKKVMEEIQQ AGNVILFIDE LHTLVGAGGA EGAIDASNIL KPALARGELQ CIGATTLDEY R KNIEKDAA LERRFQPVQV DEP

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpC

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Macromolecule #6: ATP-dependent Clp protease ATP-binding subunit ClpC

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1
Molecular weightTheoretical: 17.446889 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RLTERAQRVL AHAQEEAIRL NHSNIGTEHL LLGLMKEPEG IAAKVLESFN ITEDKVIEEV EKLIGHGQDH VGTLHYTPRA KKVIELSMD EARKLHHNFV GTEHILLGLI RENEGVAARV FANLDLNITK ARAQVVKALG NPEMSNKNAQ ASKSNNTP

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpC

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Macromolecule #7: Adapter protein MecA

MacromoleculeName: Adapter protein MecA / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 10.758939 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRIERVDDTT VKLFITYSDI EARGFSREDL WTNRKRGEEF FWSMMDEINE EEDFVVEGPL WIQVHAFEKG VEVTISKSKN EDMMNMSDD D

UniProtKB: Adapter protein MecA

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3pxi


Details: Crystal structure of the homologue ClpC-MecA complex from B.subtilis has been used as starting model, filtered at 60A.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26000
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6emw:
Structure of S.aureus ClpC in complex with MecA

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