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Yorodumi- EMDB-1017: The DnaB.DnaC complex: a structure based on dimers assembled arou... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1017 | |||||||||
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Title | The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | : / DNA helicase activity Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 26.0 Å | |||||||||
Authors | Barcena M / Ruiz T / Donate LE / Brown SE / Dixon NE / Radermacher M / Carazo JM | |||||||||
Citation | Journal: EMBO J / Year: 2001 Title: The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. Authors: M Bárcena / T Ruiz / L E Donate / S E Brown / N E Dixon / M Radermacher / J M Carazo / Abstract: Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three- ...Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face. | |||||||||
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_1017.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-1017-v30.xml emd-1017.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 1017.gif | 16.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1017 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1017 | HTTPS FTP |
-Validation report
Summary document | emd_1017_validation.pdf.gz | 201.6 KB | Display | EMDB validaton report |
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Full document | emd_1017_full_validation.pdf.gz | 200.8 KB | Display | |
Data in XML | emd_1017_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1017 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1017 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1017.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 3.6 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 : DnaB.DnaC complex from Escherichia coli
Entire | Name: DnaB.DnaC complex from Escherichia coli |
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Components |
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-Supramolecule #1000: DnaB.DnaC complex from Escherichia coli
Supramolecule | Name: DnaB.DnaC complex from Escherichia coli / type: sample / ID: 1000 Oligomeric state: one homohexamer of DnaB binds to six monomers of DnaC Number unique components: 2 |
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Molecular weight | Theoretical: 480 KDa |
-Macromolecule #1: DnaB
Macromolecule | Name: DnaB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: cytoplasma |
Molecular weight | Theoretical: 310 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: An1459/pPA569 |
Sequence | GO: DNA helicase activity / InterPro: INTERPRO: IPR001198 |
-Macromolecule #2: DnaC
Macromolecule | Name: DnaC / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Oligomeric state: three dimers / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: cytoplasma |
Molecular weight | Theoretical: 170 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: An1459/pPA569 |
-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: 7.6 Details: 50 mM Tris-HCl, 25 mM NaCl 5 mM MgCl2 2 mM DTT 0.1 mM ATP |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: double-blotting |
-Electron microscopy
Microscope | FEI/PHILIPS CM120T |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 58 / Bits/pixel: 8 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 57874 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 35 |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: SPIDER and Xmipp / Number images used: 7888 |
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