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Yorodumi- EMDB-25609: E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25609 | |||||||||
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Title | E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / DNA primase activity / DNA 5'-3' helicase / replisome ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DNA primase DnaG / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / DNA primase activity / DNA 5'-3' helicase / replisome / primosome complex / DNA replication, synthesis of primer / DNA duplex unwinding / response to ionizing radiation / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / DNA-directed RNA polymerase complex / DNA helicase activity / helicase activity / 5'-3' DNA helicase activity / 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 | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Oakley AJ / Xu ZQ | |||||||||
Funding support | Australia, 1 items
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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 AJ / Xu ZQ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25609.map.gz | 65.5 MB | EMDB map data format | |
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Header (meta data) | emd-25609-v30.xml emd-25609.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_25609.png | 68.8 KB | ||
Filedesc metadata | emd-25609.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25609 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25609 | HTTPS FTP |
-Validation report
Summary document | emd_25609_validation.pdf.gz | 543.7 KB | Display | EMDB validaton report |
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Full document | emd_25609_full_validation.pdf.gz | 543.3 KB | Display | |
Data in XML | emd_25609_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_25609_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25609 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25609 | HTTPS FTP |
-Related structure data
Related structure data | 7t22MC 7t20C 7t21C 7t23C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25609.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : E. coli DnaB DnaG C-terminal domain bound to ssDNA
Entire | Name: E. coli DnaB DnaG C-terminal domain bound to ssDNA |
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Components |
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-Supramolecule #1: E. coli DnaB DnaG C-terminal domain bound to ssDNA
Supramolecule | Name: E. coli DnaB DnaG C-terminal domain bound to ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: Replicative DNA helicase
Macromolecule | Name: Replicative DNA helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 52.406918 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGCAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI ...String: MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGCAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI AESRANKDEG PKNIADVLDA TVARIEQLFQ QPHDGVTGVN TGYDDLNKKT AGLQPSDLII VAARPSMGKT TF AMNLVEN AAMLQDKPVL IFSLEMPSEQ IMMRSLASLS RVDQTKIRTG QLDDEDWARI SGTMGILLEK RNIYIDDSSG LTP TEVRSR ARRIAREHGG IGLIMIDYLQ LMRVPALSDN RTLEIAEISR SLKALAKELN VPVVALSQLN RSLEQRADKR PVNS DLRES GSIEQDADLI MFIYRDEVYH ENSDLKGIAE IIIGKQRNGP IGTVRLTFNG QWSRFDNYAG PQYDDE UniProtKB: Replicative DNA helicase DnaB |
-Macromolecule #2: DNA primase
Macromolecule | Name: DNA primase / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA primase DnaG |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 16.664918 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: AAESGVSRPV PQLKRTTMRI LIGLLVQNPE LATLVPPLEN LDENKLPGLG LFRELVNTCL SQPGLTTGQL LEHYRGTNNA ATLEKLSMW DDIADKNIAE QTFTDSLNHM FDSLLELRQE ELIARERTHG LSNEECLELW TLNQELAKK UniProtKB: DNA primase |
-Macromolecule #3: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*...
Macromolecule | Name: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 6.038899 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ChemComp-ALF: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | 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. |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE 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. |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV 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
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Target criteria: Correlation Coefficient |
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Output model | PDB-7t22: |