+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4537 | |||||||||
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Title | E. coli DnaBC apo complex | |||||||||
Map data | apo DnaBC complex from E. coli | |||||||||
Sample |
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Keywords | Helicase / helicase loader / AAA+ / RecA / REPLICATION | |||||||||
Function / homology | Function and homology information DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / DNA 5'-3' helicase / replisome / primosome complex / DNA replication, synthesis of primer ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / DNA 5'-3' helicase / replisome / primosome complex / DNA replication, synthesis of primer / DNA strand elongation involved in DNA replication / DNA duplex unwinding / response to ionizing radiation / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / DNA helicase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 5'-3' DNA helicase activity / DNA helicase / DNA replication / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Arias-Palomo E / Puri N | |||||||||
Citation | Journal: Mol Cell / Year: 2019 Title: Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA. Authors: Ernesto Arias-Palomo / Neha Puri / Valerie L O'Shea Murray / Qianyun Yan / James M Berger / Abstract: In cells, dedicated AAA+ ATPases deposit hexameric, ring-shaped helicases onto DNA to initiate chromosomal replication. To better understand the mechanisms by which helicase loading can occur, we ...In cells, dedicated AAA+ ATPases deposit hexameric, ring-shaped helicases onto DNA to initiate chromosomal replication. To better understand the mechanisms by which helicase loading can occur, we used cryo-EM to determine sub-4-Å-resolution structures of the E. coli DnaB⋅DnaC helicase⋅loader complex with nucleotide in pre- and post-DNA engagement states. In the absence of DNA, six DnaC protomers latch onto and crack open a DnaB hexamer using an extended N-terminal domain, stabilizing this conformation through nucleotide-dependent ATPase interactions. Upon binding DNA, DnaC hydrolyzes ATP, allowing DnaB to isomerize into a topologically closed, pre-translocation state competent to bind primase. Our data show how DnaC opens the DnaB ring and represses the helicase prior to DNA binding and how DnaC ATPase activity is reciprocally regulated by DnaB and DNA. Comparative analyses reveal how the helicase loading mechanism of DnaC parallels and diverges from homologous AAA+ systems involved in DNA replication and transposition. | |||||||||
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_4537.map.gz | 8.7 MB | EMDB map data format | |
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Header (meta data) | emd-4537-v30.xml emd-4537.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4537_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_4537.png | 68.6 KB | ||
Filedesc metadata | emd-4537.cif.gz | 6.3 KB | ||
Others | emd_4537_additional.map.gz | 71 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4537 | HTTPS FTP |
-Validation report
Summary document | emd_4537_validation.pdf.gz | 262.2 KB | Display | EMDB validaton report |
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Full document | emd_4537_full_validation.pdf.gz | 261.3 KB | Display | |
Data in XML | emd_4537_validation.xml.gz | 11.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4537 | HTTPS FTP |
-Related structure data
Related structure data | 6qelMC 4538C 6qemC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_4537.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | apo DnaBC complex from E. coli | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: apo DnaBC complex from E. coli. Unsharpened map
File | emd_4537_additional.map | ||||||||||||
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Annotation | apo DnaBC complex from E. coli. Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli DnaBC apo complex
Entire | Name: E. coli DnaBC apo complex |
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Components |
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-Supramolecule #1: E. coli DnaBC apo complex
Supramolecule | Name: E. coli DnaBC apo complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 480 KDa |
-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 (E. coli) |
Molecular weight | Theoretical: 52.450945 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGFAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI ...String: MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGFAYLAEL 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 |
-Macromolecule #2: DNA replication protein dnaC
Macromolecule | Name: DNA replication protein dnaC / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 27.973152 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA MKMQRTFNRS GIRPLHQNCS FENYRVECEG QMNALSKAR QYVEEFDGNI ASFIFSGKPG TGKNHLAAAI CNELLLRGKS VLIITVADIM SAMKDTFRNS GTSEEQLLND L SNVDLLVI ...String: MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA MKMQRTFNRS GIRPLHQNCS FENYRVECEG QMNALSKAR QYVEEFDGNI ASFIFSGKPG TGKNHLAAAI CNELLLRGKS VLIITVADIM SAMKDTFRNS GTSEEQLLND L SNVDLLVI DEIGVQTESK YEKVIINQIV DRRSSSKRPT GMLTNSNMEE MTKLLGERVM DRMRLGNSLW VIFNWDSYRS RV TGKEY UniProtKB: DNA replication protein dnaC |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-...
Macromolecule | Name: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium type: ligand / ID: 5 / Number of copies: 5 / Formula: 08T |
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Molecular weight | Theoretical: 492.201 Da |
Chemical component information | ChemComp-08T: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: The grids where treated with poly-lys prior to use |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 61.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-6qel: |