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- PDB-7t22: E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP a... -

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Basic information

Entry
Database: PDB / ID: 7t22
TitleE. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA primase
  • Replicative DNA helicase
KeywordsREPLICATION/DNA / helicase / SF4 / AAA+ / REPLICATION-DNA complex
Function / homology
Function and homology information


DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DNA primase DnaG / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DNA primase DnaG / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / replisome / response to ionizing radiation / replication fork processing / DNA replication initiation / DNA-directed RNA polymerase complex / DNA helicase activity / helicase activity / DNA-directed RNA polymerase 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
DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain ...DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA primase, catalytic core, N-terminal domain superfamily / : / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA Primase, CHC2-type zinc finger / DNA helicase, DnaB type / Toprim-like / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / TOPRIM / Toprim domain profile. / TOPRIM domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / DNA / DNA (> 10) / DNA primase / Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsOakley, A.J. / Xu, Z.Q.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210100365 Australia
CitationJournal: 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
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
E: Replicative DNA helicase
F: Replicative DNA helicase
G: DNA primase
H: DNA primase
I: DNA primase
M: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,24825
Polymers370,47510
Non-polymers2,77215
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area50260 Å2
ΔGint-305 kcal/mol
Surface area127290 Å2

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Components

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Protein , 2 types, 9 molecules ABCDEFGHI

#1: Protein
Replicative DNA helicase


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 DNA primase


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 DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


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 / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli DnaB DnaG C-terminal domain bound to ssDNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli K-12 (bacteria)83333
21Escherichia coli (E. coli)562
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 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.
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 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
VitrificationInstrument: 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.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_4370: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.07particle selection
2EPUimage acquisition
4RELION3.07CTF correction
7PHENIX1.19model fitting
9PHENIX1.19model refinement
10RELION3.07initial Euler assignment
11RELION3.07final Euler assignment
12RELION3.07classification
13RELION3.073D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 657240
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46096 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation Coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00224910
ELECTRON MICROSCOPYf_angle_d0.51333777
ELECTRON MICROSCOPYf_dihedral_angle_d10.0949532
ELECTRON MICROSCOPYf_chiral_restr0.0373852
ELECTRON MICROSCOPYf_plane_restr0.0034422

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