[English] 日本語
Yorodumi
- PDB-6emw: Structure of S.aureus ClpC in complex with MecA -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6emw
TitleStructure of S.aureus ClpC in complex with MecA
Components
  • (ATP-dependent Clp protease ATP-binding subunit ...) x 5
  • Adapter protein MecA
  • Class III stress response-related ATPase, AAA+ superfamily
KeywordsCHAPERONE / Chaperone / AAA+ protein / unfoldase
Function / homologyAAA lid domain / P-loop containing nucleoside triphosphate hydrolase / 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) / Negative regulator of genetic competence (MecA) / Clp amino terminal domain, pathogenicity island component / UvrB/uvrC motif ...AAA lid domain / P-loop containing nucleoside triphosphate hydrolase / 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) / Negative regulator of genetic competence (MecA) / Clp amino terminal domain, pathogenicity island component / UvrB/uvrC motif / ATPase family associated with various cellular activities (AAA) / Clp, N-terminal domain superfamily / ClpA/B, conserved site 2 / MecA, C-terminal domain superfamily / Clp ATPase, C-terminal / ClpA/B family / Negative regulator of genetic competence, MecA / ClpA/B, conserved site 1 / Clp, N-terminal / ATPase, AAA-type, core / AAA+ ATPase domain / UVR domain / stress response to copper ion / stress response to cadmium 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
Specimen sourceStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2017 / Release: Dec 27, 2017

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3897
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC
B: ATP-dependent Clp protease ATP-binding subunit ClpC
C: Class III stress response-related ATPase, AAA+ superfamily
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
H: ATP-dependent Clp protease ATP-binding subunit ClpC
I: Class III stress response-related ATPase, AAA+ superfamily
J: ATP-dependent Clp protease ATP-binding subunit ClpC
K: ATP-dependent Clp protease ATP-binding subunit ClpC
L: ATP-dependent Clp protease ATP-binding subunit ClpC
M: ATP-dependent Clp protease ATP-binding subunit ClpC
N: ATP-dependent Clp protease ATP-binding subunit ClpC
O: Class III stress response-related ATPase, AAA+ superfamily
P: ATP-dependent Clp protease ATP-binding subunit ClpC
Q: ATP-dependent Clp protease ATP-binding subunit ClpC
R: ATP-dependent Clp protease ATP-binding subunit ClpC
S: ATP-dependent Clp protease ATP-binding subunit ClpC
T: ATP-dependent Clp protease ATP-binding subunit ClpC
U: Class III stress response-related ATPase, AAA+ superfamily
V: ATP-dependent Clp protease ATP-binding subunit ClpC
W: ATP-dependent Clp protease ATP-binding subunit ClpC
X: ATP-dependent Clp protease ATP-binding subunit ClpC
Y: ATP-dependent Clp protease ATP-binding subunit ClpC
Z: ATP-dependent Clp protease ATP-binding subunit ClpC
a: Class III stress response-related ATPase, AAA+ superfamily
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: Adapter protein MecA
f: Adapter protein MecA
g: Adapter protein MecA
h: Adapter protein MecA
i: Adapter protein MecA
j: Adapter protein MecA
k: ATP-dependent Clp protease ATP-binding subunit ClpC
l: ATP-dependent Clp protease ATP-binding subunit ClpC
m: Class III stress response-related ATPase, AAA+ superfamily
n: ATP-dependent Clp protease ATP-binding subunit ClpC
o: ATP-dependent Clp protease ATP-binding subunit ClpC
p: ATP-dependent Clp protease ATP-binding subunit ClpC


Theoretical massNumber of molelcules
Total (without water)632,28042
Polyers632,28042
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
ATP-dependent Clp protease ATP-binding subunit ... , 5 types, 30 molecules AGMSYkBHNTZlDJPVbnEKQWcoFLRXdp

#1: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 9325.732 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CA803_07045 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229LWI5, UniProt: Q2G0P5*PLUS
#2: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 25183.590 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CA803_07045 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229LWI5, UniProt: Q2G0P5*PLUS
#4: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 16426.250 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CA803_07045 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229LWI5, UniProt: Q2G0P5*PLUS
#5: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 19699.514 Da / Num. of mol.: 6
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: clpC, SAB0475 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YSD6
#6: Protein/peptide
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 17446.889 Da / Num. of mol.: 6
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: clpC, SAB0475 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YSD6

-
Protein/peptide , 2 types, 12 molecules CIOUamefghij

#3: Protein/peptide
Class III stress response-related ATPase, AAA+ superfamily


Mass: 6539.123 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpC, BN1321_130009 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1MEM2, UniProt: Q2G0P5*PLUS
#7: Protein/peptide
Adapter protein MecA /


Mass: 10758.939 Da / Num. of mol.: 6 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecA, ERS140147_01863 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A077UK83, UniProt: Q2G1U5*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: ClpC in complex with MecA from S. aureus / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

-
Processing

EM software
IDNameCategory
2EPUimage acquisition
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 26000 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
Least-squares processHighest resolution: 11 Å

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more