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Yorodumi- EMDB-5610: Structural dynamics and inter-ring communication of the MecA-ClpC... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5610 | |||||||||
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Title | Structural dynamics and inter-ring communication of the MecA-ClpC protease complex during active substrate unfolding and translocation revealed by cryo-EM | |||||||||
Map data | Reconstruction of MecA-ClpC(E280A,E618A) with ADP,MM-ADP | |||||||||
Sample |
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Keywords | unfolding / ATPase | |||||||||
Function / homology | Function and homology information negative regulation of establishment of competence for transformation / negative regulation of sporulation resulting in formation of a cellular spore / establishment of competence for transformation / sporulation resulting in formation of a cellular spore / protein-macromolecule adaptor activity / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.4 Å | |||||||||
Authors | Liu J / Mei Z / Li N / Qi Y / Xu Y / Shi Y / Wang F / Lei J / Gao N | |||||||||
Citation | Journal: J Biol Chem / Year: 2013 Title: Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine. Authors: Jing Liu / Ziqing Mei / Ningning Li / Yutao Qi / Yanji Xu / Yigong Shi / Feng Wang / Jianlin Lei / Ning Gao / Abstract: The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for ...The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5610.map.gz | 11.5 MB | EMDB map data format | |
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Header (meta data) | emd-5610-v30.xml emd-5610.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_5610_1.jpg | 191 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5610 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5610 | HTTPS FTP |
-Validation report
Summary document | emd_5610_validation.pdf.gz | 335.4 KB | Display | EMDB validaton report |
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Full document | emd_5610_full_validation.pdf.gz | 335 KB | Display | |
Data in XML | emd_5610_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5610 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5610 | HTTPS FTP |
-Related structure data
Related structure data | 3j3rMC 5607C 5608C 5609C 3j3sC 3j3tC 3j3uC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5610.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of MecA-ClpC(E280A,E618A) with ADP,MM-ADP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : MecA-ClpC(E280A,E618A)with ADP
Entire | Name: MecA-ClpC(E280A,E618A)with ADP |
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Components |
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-Supramolecule #1000: MecA-ClpC(E280A,E618A)with ADP
Supramolecule | Name: MecA-ClpC(E280A,E618A)with ADP / type: sample / ID: 1000 Details: Mutant was generated by introducing double Walker B mutations: E280A and E618A. The mutant ClpC can bind ATP but not be able to hydrolyze ATP. Oligomeric state: Hexamer of ClpC with 6 bound MecA / Number unique components: 2 |
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Molecular weight | Experimental: 600 KDa / Theoretical: 600 KDa |
-Macromolecule #1: MecA
Macromolecule | Name: MecA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Recombinant expression: Yes |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Strain: 168 |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: PET-27A |
Sequence | UniProtKB: Adapter protein MecA 1 |
-Macromolecule #2: ClpC
Macromolecule | Name: ClpC / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Strain: 168 |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: PET-27A |
Sequence | UniProtKB: Negative regulator of genetic competence ClpC/MecB |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.5 / Details: 50mM kCl, 10mM Tris-HCL,2mM MgCl2, 2mM ADP |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Sep 9, 2010 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 573 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each defocus group on 3D level |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 26037 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: MDFF |
Details | Protocol: Initial local fitting was done using Chimera and then MDFF was used for flexible fitting. ref: Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and Schulten, K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |
Output model | PDB-3j3r: |