+Open data
-Basic information
Entry | Database: PDB / ID: 8bv3 | ||||||
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Title | Bacillus subtilis DnaA domain III structure | ||||||
Components | Chromosomal replication initiator protein DnaA | ||||||
Keywords | CELL CYCLE / DnaA / DNA replication / DNA replication initiation / AAA+ superfamily / Initiator Clade | ||||||
Function / homology | Function and homology information regulation of DNA replication / DNA replication origin binding / DNA replication initiation / DNA replication / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Pintar, S. / Hubbard, J.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The bacterial replication origin BUS promotes nucleobase capture. Authors: Simone Pelliciari / Salomé Bodet-Lefèvre / Stepan Fenyk / Daniel Stevens / Charles Winterhalter / Frederic D Schramm / Sara Pintar / Daniel R Burnham / George Merces / Tomas T Richardson / ...Authors: Simone Pelliciari / Salomé Bodet-Lefèvre / Stepan Fenyk / Daniel Stevens / Charles Winterhalter / Frederic D Schramm / Sara Pintar / Daniel R Burnham / George Merces / Tomas T Richardson / Yumiko Tashiro / Julia Hubbard / Hasan Yardimci / Aravindan Ilangovan / Heath Murray / Abstract: Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is ...Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Here we show that Bacillus subtilis DnaA assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. These results provide a molecular basis for DnaA specifically engaging the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS). | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bv3.cif.gz | 244.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bv3.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bv3_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 8bv3_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 8bv3_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 8bv3_validation.cif.gz | 59 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bv3 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bv3 | HTTPS FTP |
-Related structure data
Related structure data | 8btgC 1l8qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27466.150 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dnaA, dnaH, BSU00010 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P05648 #2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.61 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation Details: Morpheus H3: 0.02 M DL-Glutamic acid monohydrate, 0.02 M DL-Alanine, 0.0 2M Glycine, 0.2M DL-Lysine monohydrochloride, 0.02M DL-Serine, 0.1 M Imidazole/ MES monohydrate pH 6.5, 20% v/v Glycerol, 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→74.399 Å / Num. obs: 56743 / % possible obs: 85.3 % / Redundancy: 9.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.06 / Rrim(I) all: 0.189 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.38→2.52 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.461 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2842 / CC1/2: 0.461 / Rpim(I) all: 0.599 / Rrim(I) all: 1.583 / % possible all: 27.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L8Q Resolution: 2.38→74.399 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 117.19 Å2 / Biso mean: 50.058 Å2 / Biso min: 19.32 Å2
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Refinement step | Cycle: final / Resolution: 2.38→74.399 Å
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LS refinement shell | Resolution: 2.381→2.443 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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