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Yorodumi- EMDB-13656: Structure of double-stranded DNA-bound MCM2-7 DH complexed with C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13656 | |||||||||||||||
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Title | Structure of double-stranded DNA-bound MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATP (3D auto-refined map) | |||||||||||||||
Map data | C1 3D auto-refinement of MD-(ATP) bound to double-stranded DNA | |||||||||||||||
Sample |
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Keywords | Helicase / Activation / Kinase / Phosphorylation / REPLICATION | |||||||||||||||
Function / homology | Function and homology information positive regulation of spindle attachment to meiosis I kinetochore / positive regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication ...positive regulation of spindle attachment to meiosis I kinetochore / positive regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / nuclear DNA replication / MCM complex binding / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / MCM complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / protein-containing complex localization / mitotic DNA replication checkpoint signaling / replication fork protection complex / mitotic DNA replication initiation / single-stranded DNA helicase activity / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / DNA replication origin binding / nuclear replication fork / subtelomeric heterochromatin formation / chromosome, centromeric region / DNA replication initiation / heterochromatin formation / DNA helicase activity / protein serine/threonine kinase activator activity / helicase activity / chromosome segregation / single-stranded DNA binding / DNA helicase / chromosome, telomeric region / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / cell division / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin binding / chromatin / signal transduction / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | synthetic construct (others) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 Å | |||||||||||||||
Authors | Saleh A / Noguchi Y / Aramayo R / Ivanova ME / Speck C | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Nat Commun / Year: 2022 Title: The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer. Authors: Almutasem Saleh / Yasunori Noguchi / Ricardo Aramayo / Marina E Ivanova / Kathryn M Stevens / Alex Montoya / S Sunidhi / Nicolas Lopez Carranza / Marcin J Skwark / Christian Speck / Abstract: The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at ...The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. Using cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6. In summary, our work provides fundamental insights into DDK structure, control and selective activation of the MCM2-7 helicase during DNA replication. Importantly, these insights can be exploited for development of novel DDK inhibitors. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13656.map.gz | 140.1 MB | EMDB map data format | |
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Header (meta data) | emd-13656-v30.xml emd-13656.xml | 32.3 KB 32.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13656_fsc.xml | 13 KB | Display | FSC data file |
Images | emd_13656.png | 56.8 KB | ||
Masks | emd_13656_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-13656.cif.gz | 9.6 KB | ||
Others | emd_13656_half_map_1.map.gz emd_13656_half_map_2.map.gz | 140.5 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13656 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13656 | HTTPS FTP |
-Related structure data
Related structure data | 7pt6C 7pt7C 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_13656.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | C1 3D auto-refinement of MD-(ATP) bound to double-stranded DNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13656_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map 1 of C1 3D auto-refinement of MD-(ATP)...
File | emd_13656_half_map_1.map | ||||||||||||
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Annotation | half-map 1 of C1 3D auto-refinement of MD-(ATP) bound to double-stranded DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 2 of C1 3D auto-refinement of MD-(ATP)...
File | emd_13656_half_map_2.map | ||||||||||||
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Annotation | half-map 2 of C1 3D auto-refinement of MD-(ATP) bound to double-stranded DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : MCM2-7 double hexamer bound to double-stranded DNA and two copies...
+Supramolecule #1: MCM2-7 double hexamer bound to double-stranded DNA and two copies...
+Supramolecule #2: synthetic double-stranded DNA
+Supramolecule #3: MCM2-7 double hexamer bound to two copies of Cdc7-Dbf4
+Macromolecule #1: synthetic double-stranded DNA
+Macromolecule #2: DNA replication licensing factor MCM2
+Macromolecule #3: DNA replication licensing factor MCM3
+Macromolecule #4: DNA replication licensing factor MCM4
+Macromolecule #5: DNA replication licensing factor MCM5
+Macromolecule #6: DNA replication licensing factor MCM6
+Macromolecule #7: DNA replication licensing factor MCM7
+Macromolecule #8: Cell division control protein 7
+Macromolecule #9: DDK kinase regulatory subunit DBF4
-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: 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 / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 1.5 seconds and blot force +2. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 3416 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |