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Yorodumi- EMDB-2334: Structural insights into the chaperone activity of Hsp40: DnaJ bi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2334 | |||||||||
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Title | Structural insights into the chaperone activity of Hsp40: DnaJ binds and remodels RepE | |||||||||
Map data | 3D Reconstruction of DnaJ:RepE54 complex | |||||||||
Sample |
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Keywords | Hsp40 / DnaJ / RepE / chaperones / protein folding / electron microscopy | |||||||||
Function / homology | Function and homology information sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein unfolding / protein-disulfide reductase activity / heat shock protein binding / viral process / unfolded protein binding / protein folding / protein-folding chaperone binding ...sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein unfolding / protein-disulfide reductase activity / heat shock protein binding / viral process / unfolded protein binding / protein folding / protein-folding chaperone binding / protein refolding / response to heat / DNA replication / protein-containing complex assembly / protein homodimerization activity / protein-containing complex / zinc ion binding / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Cuellar J / Perales-Calvo J / Muga A / Valpuesta JM / Moro F | |||||||||
Citation | Journal: J Biol Chem / Year: 2013 Title: Structural insights into the chaperone activity of the 40-kDa heat shock protein DnaJ: binding and remodeling of a native substrate. Authors: Jorge Cuéllar / Judit Perales-Calvo / Arturo Muga / José María Valpuesta / Fernando Moro / Abstract: Hsp40 chaperones bind and transfer substrate proteins to Hsp70s and regulate their ATPase activity. The interaction of Hsp40s with native proteins modifies their structure and function. A good model ...Hsp40 chaperones bind and transfer substrate proteins to Hsp70s and regulate their ATPase activity. The interaction of Hsp40s with native proteins modifies their structure and function. A good model for this function is DnaJ, the bacterial Hsp40 that interacts with RepE, the repressor/activator of plasmid F replication, and together with DnaK regulates its function. We characterize here the structure of the DnaJ-RepE complex by electron microscopy, the first described structure of a complex between an Hsp40 and a client protein. The comparison of the complexes of DnaJ with two RepE mutants reveals an intrinsic plasticity of the DnaJ dimer that allows the chaperone to adapt to different substrates. We also show that DnaJ induces conformational changes in dimeric RepE, which increase the intermonomeric distance and remodel both RepE domains enhancing its affinity for DNA. | |||||||||
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_2334.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-2334-v30.xml emd-2334.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd2334.jpg | 35.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2334 | HTTPS FTP |
-Validation report
Summary document | emd_2334_validation.pdf.gz | 207.6 KB | Display | EMDB validaton report |
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Full document | emd_2334_full_validation.pdf.gz | 206.8 KB | Display | |
Data in XML | emd_2334_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2334 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2334 | HTTPS FTP |
-Related 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_2334.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D Reconstruction of DnaJ:RepE54 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.33 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 : DnaJ:RepE54 complex
Entire | Name: DnaJ:RepE54 complex |
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Components |
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-Supramolecule #1000: DnaJ:RepE54 complex
Supramolecule | Name: DnaJ:RepE54 complex / type: sample / ID: 1000 Oligomeric state: One dimer of DnaJ binds to two monomers of RepE Number unique components: 2 |
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Molecular weight | Experimental: 140 KDa / Theoretical: 140 KDa / Method: Analytical ultracentrifugation (AU) |
-Macromolecule #1: Hsp40
Macromolecule | Name: Hsp40 / type: protein_or_peptide / ID: 1 / Name.synonym: DnaJ / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: cytoplasm |
Molecular weight | Experimental: 80 KDa / Theoretical: 80 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Chaperone protein DnaJ |
-Macromolecule #2: replication initiator protein RepE54 of plasmid mini-F
Macromolecule | Name: replication initiator protein RepE54 of plasmid mini-F type: protein_or_peptide / ID: 2 / Name.synonym: RepE54 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: cytoplasm |
Molecular weight | Experimental: 30 KDa / Theoretical: 30 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.4 Details: 20mM Hepes pH 7.4, 50mM KCl, 5mM DTT and 0.1mM EDTA |
Staining | Type: NEGATIVE Details: Samples (either DnaJ:RepE, DnaJ:RepE1-144 or DnaJ:RepE54 complexes) were diluted 1:100 in 20mM Hepes pH 7.4, 50mM KCl, 5mM DTT and 0.1mM EDTA buffer, applied onto carbon-coated copper grids ...Details: Samples (either DnaJ:RepE, DnaJ:RepE1-144 or DnaJ:RepE54 complexes) were diluted 1:100 in 20mM Hepes pH 7.4, 50mM KCl, 5mM DTT and 0.1mM EDTA buffer, applied onto carbon-coated copper grids and stained with 2% uranyl acetate. |
Grid | Details: 300 mesh Cu/Rh grid with thin carbon support and glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 1200EXII |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Feb 2, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 340 / Average electron dose: 10 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal magnification: 60000 |
Sample stage | Specimen holder: JEOL 1200EXII / Specimen holder model: JEOL |
-Image processing
Details | The particles were selected by manual picking |
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CTF correction | Details: CTFFIND |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, XMIPP / Number images used: 9612 |
Final two d classification | Number classes: 75 |