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Yorodumi- EMDB-2508: Nucleotide and partner-protein control of bacterial replicative h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2508 | |||||||||
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Title | Nucleotide and partner-protein control of bacterial replicative helicase structure and function | |||||||||
Map data | Aquifex aeolicus DnaB replicative helicase | |||||||||
Sample |
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Keywords | DnaB / helicase / RecA / DNA replication / ATPase / Aquifex aeolicus | |||||||||
Function / homology | Function and homology information primosome complex / DNA replication, synthesis of primer / DNA duplex unwinding / DNA unwinding involved in DNA replication / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Aquifex aeolicus (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Strycharska MS / Arias-Palomo E / Lyubimov AY / Erzberger JP / O'Shea VL / Bustamante C / Berger JM | |||||||||
Citation | Journal: Mol Cell / Year: 2013 Title: Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Authors: Melania S Strycharska / Ernesto Arias-Palomo / Artem Y Lyubimov / Jan P Erzberger / Valerie L O'Shea / Carlos J Bustamante / James M Berger / Abstract: Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple ...Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple methods to investigate the bacterial replicative helicase, DnaB. A 3.3 Å crystal structure of Aquifex aeolicus DnaB, complexed with nucleotide, reveals a newly discovered conformational state for this motor protein. Electron microscopy and small angle X-ray scattering studies confirm the state seen crystallographically, showing that the DnaB ATPase domains and an associated N-terminal collar transition between two physical states in a nucleotide-dependent manner. Mutant helicases locked in either collar state are active but display different capacities to support critical activities such as duplex translocation and primase-dependent RNA synthesis. Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors. | |||||||||
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_2508.map.gz | 154.4 KB | EMDB map data format | |
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Header (meta data) | emd-2508-v30.xml emd-2508.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_2508.png | 56.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2508 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2508 | HTTPS FTP |
-Validation report
Summary document | emd_2508_validation.pdf.gz | 192.9 KB | Display | EMDB validaton report |
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Full document | emd_2508_full_validation.pdf.gz | 192.1 KB | Display | |
Data in XML | emd_2508_validation.xml.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2508 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2508 | 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_2508.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Aquifex aeolicus DnaB replicative helicase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.36 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 : Aquifex aeolicus DnaB replicative helicase
Entire | Name: Aquifex aeolicus DnaB replicative helicase |
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Components |
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-Supramolecule #1000: Aquifex aeolicus DnaB replicative helicase
Supramolecule | Name: Aquifex aeolicus DnaB replicative helicase / type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 1 |
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Molecular weight | Theoretical: 322 KDa |
-Macromolecule #1: Replicative DNA helicase
Macromolecule | Name: Replicative DNA helicase / type: protein_or_peptide / ID: 1 / Name.synonym: DnaB / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
Molecular weight | Theoretical: 53.6 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Replicative DNA helicase |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50 mM HEPES pH 7.5, 200 mM KCl, 5% Glycerol, 5 mM MgCl2, 1 mM ADP-BeF3 |
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Staining | Type: NEGATIVE / Details: 2% (w/v) uranyl acetate |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Jun 29, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.3 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 49000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: Each micrograph |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: EMAN2, SPARX / Number images used: 38702 |