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Yorodumi- PDB-7t22: E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t22 | ||||||
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Title | E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 | ||||||
Components |
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Keywords | REPLICATION/DNA / helicase / SF4 / AAA+ / REPLICATION-DNA complex | ||||||
Function / homology | Function and homology information DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DNA primase DnaG / DNA helicase complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / DNA primase activity / DNA replication, synthesis of primer ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DNA primase DnaG / DNA helicase complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / DNA primase activity / DNA replication, synthesis of primer / replisome / DNA duplex unwinding / response to ionizing radiation / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / DNA helicase activity / DNA-directed RNA polymerase complex / helicase activity / DNA helicase / DNA replication / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Oakley, A.J. / Xu, Z.Q. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli Authors: Oakley, A.J. / Xu, Z.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t22.cif.gz | 526.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t22.ent.gz | 441.4 KB | Display | PDB format |
PDBx/mmJSON format | 7t22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/7t22 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/7t22 | HTTPS FTP |
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-Related structure data
Related structure data | 25609MC 7t20C 7t21C 7t23C M: map data used to model this data 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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-Components
-Protein , 2 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 52406.918 Da / Num. of mol.: 6 / Mutation: F103C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dnaB, groP, grpA, b4052, JW4012 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RecA- / References: UniProt: P0ACB0, DNA helicase #2: Protein | Mass: 16664.918 Da / Num. of mol.: 3 / Fragment: C-terminal domain / Mutation: R568C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dnaG, dnaP, parB, b3066, JW3038 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RecA- / References: UniProt: P0ABS5, DNA primase DnaG |
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-DNA chain , 1 types, 1 molecules M
#3: DNA chain | Mass: 6038.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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-Non-polymers , 3 types, 15 molecules
#4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-ALF / #6: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E. coli DnaB DnaG C-terminal domain bound to ssDNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Buffer solution | pH: 7.6 Details: 20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP. | ||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Details: Grids covered with a 2 nm continuous carbon film. Glow-discharged grids were floated on 40 microL drops of a 0.1% (w/v) aqueous solution of poly-lysine hydrobromide (MW 30-70 kDa; ...Details: Grids covered with a 2 nm continuous carbon film. Glow-discharged grids were floated on 40 microL drops of a 0.1% (w/v) aqueous solution of poly-lysine hydrobromide (MW 30-70 kDa; Polysciences, Inc.) for two min, briefly rinsed with MilliQ water 4 times and then allow to air dry. Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 279 K Details: 3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_4370: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 657240 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46096 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: Correlation Coefficient | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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